Poisoned Trust
by Link III
Summary: Formerly the Metroid Fusion Interactive Story. A conspiracy running deep throughout the Federation...a threat that could end life as we know it...and the shadow of the ever-growing Pirate Empire. Samus's final mission awaits.
1. Part 1

**A brief word about the structure of this story before we begin.**

**This story began as the Metroid Fusion Interactive Story on the GameFAQs message boards. Originally, readers of the story would vote on the path the story would take to influence its plot. Each line break denotes the beginning of a new section of the story.**

**In addition to this, I would occasionally post supplementary material, such as my interpretations of the Metroid universe and explanations that didn't quite fit into the main story, but were important anyway.**

**...Well, I think that's it. Enjoy!**

**

* * *

**

The entire family was crammed onto the couch, staring absentmindedly at the television. It was a relatively old set; the holographic screen required actual interaction, unlike the voice-commanded sets that were the standard nowadays. The family was watching a documentary about human life before interstellar travel was possible, an extremely educational experience. One of the primary people who had contributed to the documentary, Homer Simpson, was now on-screen.

"I had no idea that humans had yellow skin before space travel," the father of the family mused. "It's amazing what you learn from these things."

Just as Homer was about to strangle Bart, the television switched to the news.

"We interrupt this program to bring you a special news report. Bounty hunter Samus Aran, famed for stopping the Space Pirates time and time again, has turned on the Galactic Federation. We're here live with Federation President Martin Rodriguez for an exclusive interview."

The camera panned to Rodriguez. The Federation president, a grim-faced human, waved slightly.

"President Rodriguez, what are the details of Aran's betrayal?"

His face was devoid of any emotion, and he replied in a way that implied that he had rehearsed it. "As I'm sure you know, the Biologic Space Laboratories were focused on discovering ways to help the galaxy. We were directly on the verge of an important discovery when Aran infiltrated the station, bent on destroying all that we had created. She jettisoned the section containing the experiments, and then, ensuring that we couldn't replicate it, crashed the BSL into the surface of SR388, obliterating both the station and the planet."

The camera panned back to the reporter, a Wred. Wreds, being the third species to join the Galactic Federation (the first being humans, and the second being the Chozo), were highly respected across the galaxy…however, they were extremely nosy, which was why most of them sought jobs as reporters. They were a humanoid species, with red skin, eyes located high on their foreheads, and a downy hair covering most of their torso. They had no sense of smell, and their hearing was less than ideal. They made up for this, however, with their extremely accurate eyes.

"I see," he said. "Could you possibly tell us a bit about Aran's past?"

Rodriguez nodded. "Certainly."

He cleared his throat. "Aran's home planet was K-2L, which, as you may recall, was attacked by the Space Pirates twenty-five years ago. Aran was four years old at the time. Her parents were murdered by the Space Pirates, but what became of her after that is unclear.

"Ten years later, she reappeared, donning a Chozo battle suit. While she claims that the Chozo found and raised her, the fact that the Space Pirates conducted a raid on the Chozo colony of Zebes several days earlier lent credence to the theory that she may have been raised by the Pirates themselves."

The Wred's eyes lit up. "So, you think she was raised as a Space Pirate? But hasn't she been your trump card in defeating the Space Pirates for years now?"

Rodriguez nodded. "Yes, she has. We believe, however, that this was merely an act to gain our trust. Aran could act as a spy from the inside, feeding the Space Pirates information about our operations. Now, if I may continue…"

The Wred nodded. "Of course."

"Thank you. Anyway, Aran reappeared in a Chozo battle suit. She first enlisted in the Galactic Federation Marine Corps. She was quite effective, but she resigned when her CO, Adam Malkovich, was killed."

"Adam Malkovich? Could you possibly tell us more about this?"

"Classified info," Rodriguez responded dryly.

"Of course. Continue."

"As I'm sure many of you know, seven years ago, the Galactic Federation discovered a species on SR388, which we named Metroids. They could suck the life energy out of any living creature, leaving them a lifeless husk. Obviously, such a creature was incredibly dangerous, so we prepared to transfer them to a secure facility. On the way, however, we were attacked by Space Pirates. They took the Metroids, and began mass-breeding them on planet Zebes. We sent Aran, who, at that time, was the most proficient bounty hunter there was. She successfully wiped out the Pirates' Metroids, and disabled the Mother Brain."

"There are some rumors that the Aurora Units that Galactic Federation society is based around are based on Mother Brain," the Wred said. "Can you confirm this?"

"No comment," replied Rodriguez.

"After this came the Phazon incident, which I'm certain none of us need to remember. After this, we realized that Metroids needed to be wiped out. We sent a Federation squadron to execute the task, but they weren't up to it. Aran once again was needed to finish the job."

"However, she didn't finish it entirely. She allowed one infant Metroid to live – most likely because of her Pirate alliance. She handed it over to Federation authorities, but she most likely contacted the Space Pirates beforehand. Not three minutes passed after Aran had left before the colony was attacked and the Metroid stolen. She once again presumably ended Pirate operations, but this time, she also ended up blowing up planet Zebes."

"Later, she reappeared aboard the BSL, but this time there was something different about her: she had infused herself with Metroid DNA. Her reasoning for this is uncertain, and -"

"Ah," the Wred said suddenly, "but an insider report says that Aran was infused with the Metroid DNA by the Federation themselves, in order to eradicate a parasite from her system."

Rodriguez remained expressionless. "I can assure you, this 'insider' has no idea what they're talking about. Anyway, due to evidence of Pirate DNA found in the wreckage, we believe that Aran also let Space Pirates aboard, in order to capture the only remaining DNA specimen of one of their commanding officers, Ridley."

The Wred turned back toward the camera. "Aran is very dangerous. Should you see her anywhere, do not attempt to confront her; instead, call Federation authorities and -"

Click.

Thousands and thousands of miles away, in the vast regions of space, Samus Aran glared at the now blank holographic display, seething. How dare they…suggesting that she was allied with those…monsters…

"Calm down," Adam said. "There's nothing we can do about it."

Samus sat back in the cockpit of her ship. "Right," she replied. "The most we can do right now is evade capture and try to find any remaining evidence. The BSL couldn't have been the Federation's only Metroid breeding facility."

The ship's computer was Adam Malkovich himself, his mind having been uploaded to a computer before death.

"We should probably focus on evacuating Federation space, first," Adam said. "While we're here, we're constantly in danger."

* * *

"I guess you're right," Adam conceded. "But be sure to maintain a low profile."

Samus nodded. "Of course. I'm not that stupid."

"Right. Anyway, the nearest Federation vessel is the G.F.S. Empyrean, stationed near the planet Lycas. I doubt that they're storing Metroids on a military vessel, though."

"What about the planet itself?"

Adam contemplated this for a bit. "Well, Lycas is a rather cold planet…it would be ideal for keeping Metroids without the risk of them attacking. I'm not sure if it's such a good idea to head there, though. We'd have to pass right by the Empyrean, and you've seen Federation ships before…they're capable of utterly destroying us without any effort whatsoever."

Samus frowned. "You're right…" Sighing, she slumped down and stared out the window.

Suddenly, she snapped her fingers. "That's it!"

"What's it?" asked Adam.

"We use a Federation ship to get by!"

If Adam still had a body, he would have been staring at Samus in disbelief.

"There's just one problem, Samus…_we don't have a Federation ship._"

There was a broad grin on Samus' face. "Yes we do."

-=-=-

Rodriguez collapsed into his seat, exhausted. It had been quite a day…every reporter in the galaxy, it seemed, was hard-pressed on getting him to divulge his plans to deal with Samus. Of course, he couldn't do that; not with the television network available from literally every location in the galaxy, anyway…

He wondered why Aran's ship computer hadn't contacted him yet. Yes, it WAS the mind of Adam Malkovich, but it shouldn't have retained any memories during the transfer process. It was completely loyal to the Federation. Could Aran have hacked it? No, that was impossible. They used the highest encryption possible to protect the Federation computers. She must have befriended him again, then. He'd have to make a note of erasing emotion from the rest of uploaded minds.

He glanced down at his desk. Hidden in that desk were the papers detailing every experiment they were working on in the Federation…he smiled sardonically. If only Aran knew exactly what they were researching, she would have tried to crash the BSL into the Galactic Federation capital itself, not SR388.

He picked up his phone and dialed a number into it. "This is Galactic Federation president Martin Rodriguez. Requesting General Arvo of the G.F.S. Scheria. Repeat, requesting General Arvo."

There was a pause, and then a soft voice reached his ears. "Greetings, President."

"Arvo," he greeted. "You're currently near the Klar nebula, correct?"

There was another pause. "I am."

"You may recall that, several years ago, the G.F.S. Valhalla went missing there, but was later rediscovered. We recently sent a team there to conduct some experiments…but Samus Aran knows where it is. It's still able to fly, so she might decide to head there to take command of it so she can deceive other vessels. The team there is top-secret, so she doesn't know that they're there…I doubt that she'll spare them once she finds out, though. The Valhalla's weapons systems no longer work, so I want you to protect it. Make sure she doesn't board the Valhalla, and, if possible, kill her. Is that clear?"

"Yes, it is. Aran won't get by me, President. Good day."

Arvo hung up.

-=-=-

"The G.F.S. Valhalla," Samus read aloud, "went missing four years ago while in a training mission in the Klar nebula. The ships logs revealed that it had been attacked by Space Pirates. The ship's Aurora Unit, 313, was stolen. Five months later, the Valhalla was rediscovered. Samus Aran investigated the Valhalla, discovering a code that helped the Federation – oh, HELPED them? More like did all the work…anyway, helped the Federation resolve the Phazon crisis. After this, the Klar nebula became off-limits to everyone without a proper license. The G.F.S. Valhalla still stays there, empty, a monument to those the Federation has lost in its struggle against the Space Pirates."

"So, we're going to use the Valhalla to disguise ourselves? Won't people know that it's supposed to be off floating in space without a crew?"

Samus shrugged. "The Federation keeps plenty of secrets. We can just say that they decided to reinstate the Valhalla."

"Fair enough," Adam replied. "First, though, what should we do with _them?_"

Samus glanced at the back of the ship, where the Etecoons and Dachoras, the small monkey-like and ostrich-like creatures, respectively, that had helped her out several times now, were sleeping. She frowned, lines creasing her forehead. As long as they were with her, they were in constant danger…but there was no place that she could let them go where she wouldn't be captured. "Adam," she said. "We're going to have to keep them with us. Keep their safety your number one priority. If, at any point, it looks as if we're going to be killed or captured, get them into the escape pod and launch it. That's the best I can do."

She still felt slightly guilty, though. She wished she could do something more for them.

"Right, then. I'll give you the coordinates," she said. She punched the numbers in and activated the thrusters. "Autopilot is on…all systems stable…let's go."

The ship flew into the distance.

"Engage the hyperdrive…"

She pressed a button, and, suddenly, everything around them was filled with neon colors, a sign that they had entered hyperspace.

The galaxy was enormous, obviously, so it wasn't conventional to fly around normally. Luckily, when Contact was first made, the people of Aliehs III, the Eyfin, known for their ship-making technology, had already devised a solution: a way to create rifts in the fabric of space, making shortcuts to every place in the galaxy.

They exited hyperspace within a few minutes, the Valhalla visible in the distance, just a short distance away.

The problem was, there was another ship there, as well.

* * *

"Activate ship cloaking!" Samus ordered immediately. Within seconds, her ship had disappeared off any radar. "Did they see us?" she asked.

"Not on the radar, I'd wager, but pray that all of their troopers are nearsighted," Adam replied grimly. Unfortunately for them, this didn't seem to be the case; the ship was slowly, but deliberately, moving in their direction.

Samus swore and pressed a button to her right. A blast shield enclosed the ship. While it wouldn't provide sufficient protection against a Federation ship, it was better than nothing. The downside was that she would have to rely entirely on her radar to navigate.

"Incoming transmission," Adam said suddenly.

With a crackle of static, the radio controls went online. "Aran," a soft, cold voice greeted. "This is General Arvo aboard the G.F.S. Scheria. As I'm sure you know, this ship can annihilate yours in a single blast. I do not wish to kill you, but if you do not surrender this instant, you leave me with no other option. If you do surrender, you will be given a fair trial in Galactic Federation court."

Samus snorted. "A fair trial, you say? Could you possibly give me more details?" As she said this, she maneuvered her ship to face the Valhalla, and, for a brief instant, started her thrusters, then turned them off again. This caused her to begin drifting slowly towards the Valhalla.

"Stalling us will gain you nothing."

"Let me ask you something, General: are you aware of the experiments the Federation was conducting aboard the B.S.L.?"

"Stalling will gain you nothing," repeated Arvo.

"They were -"

She didn't have a chance to finish her sentence, as the transmission abruptly ended. Briefly opening the blast shield, she saw the Scheria charging its weapons. "Adam! Reroute all energy to shield and fuel systems!" Samus ordered.

"Right away, lady," said Adam, quickly complying. Samus reactivated the thrusters and headed in the direction of the Valhalla.

Suddenly, her ship was knocked off course. The Etecoons and Dachoras awoke with a yelp. "What in the name of…?" A quick glance at her radar revealed that she was being flanked by two smaller Federation fighters. One of them had rammed into her ship. "No hull damage," reported Adam.

Samus gritted her teeth and continued on her path, trying her best to outmaneuver the Federation fighters. The Scheria hadn't fired yet; it must've been waiting for a clear shot.

"Adam," she said suddenly. "About how long could I survive in space at the current oxygen levels in my suit?"

"Around three minutes," he replied, "possibly four. Why?"

She ignored his question. "The ship's databanks can be transferred from one vessel to another, can't they?"

"Yes," he answered. "What are you planning?"

Samus stood up, putting the ship on autopilot. "Depending on how you look at this, it could be either incredibly smart or completely idiotic. Your choice."

She walked over to the hatch of the ship. "When I give the signal, transfer the databanks to the Federation fighter on the right, and get the Etecoons and Dachoras into the escape pod. You'll know what the signal is."

With that, she ejected herself from the ship.

-=-=-

Out in space, Samus was aware of just how vulnerable she was. One push in the wrong direction, and she would be sent careening into the depths of space with almost no hope of return. With this unpleasant thought in mind, she pushed off toward the nearest Federation fighter.

They really were idiots, she observed. They were so focused on the ship itself that they had failed to notice that she wasn't in it anymore. There was a hatch on the underside of each fighter, which was convenient enough; it could be manually activated. Indeed, with relatively little trouble, she was able to gain access to the fighter.

When the trooper piloting the fighter finally heard the hiss of the hatch opening, it was too late; Samus already had her arm cannon pointed directly at his head. "If you don't follow my instructions exactly, you are going to die," she stated calmly. "First, establish contact with my ship."

Shakily, the trooper opened a communication with it, Samus observing his actions like a hawk.

"Adam," Samus said. "I've hijacked this Federation fighter. End autopilot and prepare to eject the Etecoons and Dachoras."

"Right away," came the reply, and the com link closed.

"Now, contact your buddy over there and the Scheria and tell them that my ship has run out of fuel, but I refuse to come quietly."

The trooper opened a link. "W-Wesley here. Aran's ship has run out of fuel. Repeat, A-Aran's ship has run out of fuel. She refuses to come quietly."

General Arvo's voice responded. "Affirmative. We'll just dispatch of her, then. Evacuate the area."

Knowing that she had precious little time before her ship was blown to bits, Samus reopened the com link with Adam. "Transfer the databanks and eject the escape pod immediately!" she ordered. She didn't wait for a response, and turned to the trooper again.

"Do you believe me to be guilty?" she asked, recalling Adam's words to her a few days earlier.

Slowly, the trooper nodded. Sighing, Samus turned away.

Moments later, her ship exploded in a fiery display.

"Adam, are you there?" she asked. There was a tense moment of silence.

"Affirmative, lady. We lost a bit of information, but nothing too important."

"Good. Disable all com links."

She turned back to the Federation trooper. "You," she said. "What's your name?"

"T-Tarus W-Wesley," the trooper responded.

"Well, Tarus Wesley," Samus said, "whether you think I'm guilty or not – and I'm going to prove that I'm not, by the way – you're going to help me."

"H-help…you?"

Samus pressed her arm cannon against his head again. "Yes, because if you don't, you're going to die. It's your call."

"…All right. I don't really have a choice, do I?"

Samus smirked. "Smart," she said.

* * *

**Extra #1 : Sphere Keys**

Sphere keys have become the standard in locking mechanisms in recent years. Originally created by the Yaafgols of Arista VII, the keys, each encoded with a lengthy combination of letters, numbers, and textures, react only with their respective locks. The Space Pirates have adapted this technology, as well, and one of their chief projects is creating a universal sphere key. These endeavors, so far, have been unsuccessful.

The Chozo, realizing that their warriors might be required to break into various facilities, were the only ones to figure out how to create such a universal key. This key, known as the "Morph Ball" (Maru Mari in their language), actually changes one who uses the Chozo Battlesuit into a ball. They are then capable of detonating special bombs, which can circumvent any sphere key lock. The Morph Ball technology is an enigma to all but the Chozo, and baffles even Samus Aran herself.

The Space Pirates base their attempts at creating a universal sphere key on the Morph Ball; however, since they have been unable to capture Samus, it is currently impossible for them to research it thoroughly.

* * *

"Enable the communication links again," Samus told Adam.

"…Wesley? Wesley, do you read?"

Tarus Wesley quickly moved over to the communications device, still uncomfortably aware of Aran's arm cannon. "Wesley here. I read you loud and clear, General."

"What happened? We lost communication with you for a minute there."

"Just some minor technical difficulties," Wesley replied. "Everything's fine."

"Good," said General Arvo. "Return to the ship. You'll be well-rewarded for your help."

Samus froze.

She hadn't thought of that. If she was discovered…

"Quick," she whispered. "Is there a cargo hold here?"

Silently, Wesley pointed to the back wall. There was an indent for a key there. Wesley was about to hand Samus the key, but she had disappeared.

Confused, he looked around for her before hearing something rolling around on the ground. He gave a start when he saw an orange sphere, slightly less than a meter tall, roll over to the lock, jump up into it, and detonate an explosive. The explosive circumvented the lock, and the cargo hold doors opened.

"…That works," muttered Wesley, shutting the cargo hold door after Samus had wedged herself comfortably in between two crates.

"Right, then…um…computer?"

"The name is Adam," it replied coolly.

"Adam, right…I'll just be heading back to the Scheria, all right?"

"Fine. But rest assured, I'll be watching you. If you do anything to betray Samus, you'll be sorry. You'd be surprised at what a computer can do…"

"Er, sure. I'll keep that in mind." He began manning the controls, and headed back to the ship…

-=-=-

The G.F.S. Scheria, a Vulcan-class battleship, was imposing not only on the outside, but on the inside as well. General Arvo had put his personal touches on the ship; odd statues lined the halls, depicting Space Pirates in various states of torture. While people agreed that the pirates would deserve such fates, the statues were still rather disturbing. One particularly grotesque one depicted a Space Pirate's intestines being pulled out, then wound tightly around its throat.

Yes, General Arvo was certainly uplifting to be around.

Wesley was escorted by two silent troopers. Most of the ship personnel didn't talk much; they had long since learned that idle chit-chat was frowned upon by the general.

"The general's just inside," one of the troopers grunted when they had reached the command bridge. "Go on."

Wesley took a deep breath and entered. Arvo was sitting, his back to the door. "I'm here, sir," said Wesley. General Arvo turned around.

The familiar Space Pirate general smiled.

"Tarus Wesley…" he murmured. "You're here. Good. I've already given the other one who helped his reward…I daresay that you're in for a promotion. I do wonder why Aran chose only to tell you that she wouldn't surrender, though…no matter. You are promoted to the rank of Commander…a high honor, indeed. I daresay my own kind will contact me soon enough, though," Arvo added with a scowl.

Wesley nodded. "Yes, of course. They've been trying to kill Aran for years, and your ship succeeded…"

"Yes, well," Arvo said, pressing a button on his chair to use its wheels, "you'd better get going…Commander Wesley. I'm sure you'd like to find out what you can do with your new rank."

-=-=-

"So, what has Wesley done so far?" asked Samus, speaking to Adam.

"Well, he's been promoted to the rank of Commander by General Arvo…speaking of which, do you know what species he is?"

Samus frowned. "No, why?"

"He's a Space Pirate."

Samus jumped up in shock. "What?! Why would the Federation have a Space Pirate as a general? …And on that note, why is a navy officer a general…?"

"Don't ask me," Adam replied. "I don't have access to the Federation's main database anymore. The things that I downloaded before being cut from it don't include anything about him."

Samus sighed. "It figures. Well, either way, we should collect any data that we can. I am curious as to why the Federation is guarding the Valhalla…there wasn't anything important there last time I went there…"

"Well, with Wesley's new rank, we should probably be able to gain access to it. Ah, here he comes now."

Right on cue, Wesley entered the fighter. "Hello," greeted Samus. "So, I heard you got a promotion for 'killing me'."

Wesley stared in surprise. "How did you…?"

"Adam's been monitoring your progress," explained Samus. "He isn't able to speak to you directly, but he can see and hear everything that you do."

Wesley frowned. "I don't get any privacy, do I?"

"None," Adam confirmed. "Anyway, we need you to do us a favor. Get us onto the Valhalla. We want to know what the Federation's been doing there."

Wesley looked at Samus questioningly. "What do you mean, what the Federation's been doing there?"

Samus sighed. "The Federation," she explained, "may not be quite as benevolent as you think it to be. If we find anything there, it should be self-explanatory. If not, I'll tell you exactly what happened on the B.S.L."

"Fair enough," Wesley replied. "I'll see if I can get you on there."


	2. Part 2

**Extra #2: General Arvo**

Space Pirates who show any sign of cowardice shall be hunted down.

This is the law by which all Space Pirates live their lives. Unit 1337, known to his peers as "Arvo", learned this firsthand thirty years ago. Details regarding the incident are hazy, but it has been confirmed that something happened on the dwarf planet of Pluto. A Federation fleet discovered a pod floating in space. Within it was a half-dead Arvo. Despite him being a Space Pirate, protocols required that any injured bioforms who were not harmed as a result of the Federation be helped in any way possible.

Against all odds, Arvo survived. A pariah to the Space Pirates at that point, due to circumstances which nobody fully understands, he had no choice but to join the Federation. Arvo was immensely helpful in the battles that ensued from that point onward. Being a moderately high-ranking Space Pirate, he had exclusive knowledge of Space Pirate strongholds and experiments, and with Arvo's help, the Pirates were completely driven out of over 300 solar systems. Eventually, Arvo joined the military in order to help more - the biggest mistake of his life.

Arvo rose through the ranks, eventually becoming a general. During a battle on the planet of Aarat XIV, he encountered his former squad - an unpleasant surprise, to be sure. The ensuing battle had them completely ignoring the Federation troopers and attacking only him. Eventually, they succeeded in permanently damaging both of his legs. At that point, backup arrived, and he was spared any further injury.

Arvo chose to remain in a military position, giving orders instead of fighting in battle. He was transferred to the G.F.S. Scheria, but he requested to keep his title of General instead of Admiral. Since then, he has bore a bitter grudge against his own kind - a grudge which shows up quite prominently in the halls of the Scheria.

* * *

"Commander Tarus Wesley to G.F.S. Valhalla. Valhalla, do you read?"

There was a crackle of static, then a response.

"G.F.S. Valhalla's lead scientist, Al Enstin to Commander Tarus Wesley. What can I do for you, Commander?"

"I've been ordered to search the Valhalla for any sign of the experiments being tampered with. Samus Aran was recently killed around here, but we need to make sure that she didn't do anything beforehand."

"Of course, Commander. Come on aboard."

Wesley smiled slightly. "Thank you."

He maneuvered the ship into the Valhalla's docking bay, and picked up his "sphere key" – which was, of course, Samus Aran in morph ball form. Despite its size, it was surprisingly light, like all sphere keys. As long as Samus didn't move around, no one would be able to tell the difference.

As Wesley exited the ship, several soldiers stationed there saluted. "Greetings, Commander. You may leave your sphere key here; we'll guard it well."

Wesley frowned, shaking his head. "No, thank you. I'd feel much safer if I brought it with me."

The soldier shrugged. "Suit yourself. Anyway, just give us your pass onto the ship, and you're good to go."

Wesley froze.

"My pass?" he repeated dumbly.

"Yep. The one you were given when you were given the assignment. You didn't lose it, did you?"

"Uh…yes, that must've been what happened. I lost it," he said, laughing nervously. "That isn't a problem, is it?"

"No, you should be fine. All I need to do is contact the president and -"

"No!"

The soldier frowned, looking up at Wesley suspiciously. "What do you mean, no…?"

"I mean…no, it's okay. I'll find my pass again on my own."

The soldier continued staring. "Are you sure that you even HAVE a pass…?"

Things were quickly spiraling out of Wesley's control.

The soldier paused suddenly, as he received a radio signal. "One moment," he said.

"…Yes. …Ah! Hello, sir…yes, he's right here…oh, really? Sorry…I had no idea…right. Goodbye, sir."

The soldier looked back up. "That was the president," he said. "He wanted to let me know that I was to let you pass. You have access to everything on the ship. That's a great honor, you know…even the people working here don't have that privilege…"

Dumbfounded, Wesley let himself be escorted by the soldier through the doors.

-=-=-

"Commander Wesley, an honor to meet you in person. I'm Al Enstin. We've talked briefly via radio, of course."

Wesley nodded. "Pleasure to meet you too. Now, then…I'd like to begin with your most top-secret experiments. Get them out of the way first, you see."

Enstin looked nervous. "Yes, those. Of course."

He walked over to a large door, reinforced with the hardest metals in the galaxy, double-bolted, with an eye-scanner, a hand-scanner, and a sphere key lock, all of which had to be activated for the door to open. After that, there would be a DNA verification scan before entry would be granted. Clearly, the Federation wanted almost no one to know about this.

The hall was lined with large stasis tubes, most of which were empty.

"I'd prefer to see this by myself," Wesley said to Enstin.

"Right," Enstin replied. "I'll wait for you just outside."

Wesley walked down the hall, his footsteps echoing down it. Aside from himself, the room was completely quiet. He noted that he could hear his heart beating.

Suddenly, as he turned the corner, the morph ball jumped out of his arms and turned into the familiar shape of Samus Aran.

"I'll lead from here," she said curtly. Wesley nodded, his heart racing.

And suddenly, the empty tubes gave way to thousands of full ones.

All of them were filled with humans.

As they walked by the tubes, however, the humans became less and less recognizable. Every now and then, Samus would pause, press a button on her helmet, and stare at the contents of a tube before continuing onward. Wesley would pause and simply look at them.

One human had spikes growing out of his back. Another had coarse fur coating his entire body. Yet another bore a wolf-like snout, sharp teeth lining her mouth.

"What is this stuff?" he asked Samus.

"Federation experiments," she replied grimly. "I had my suspicions when they infused me with Metroid DNA, but I had no idea that they had already gone this far…"

They continued walking down the endless rows, as the humans they passed became more and more disfigured. At one point, five in a row were writhing in clearly visible agony. Their mouths were open, but they were unable to scream. Wesley felt sick all of a sudden.

"Can we head back now, please?" he asked.

"Not yet," Samus replied. "I want to see everything."

Suddenly, the soft blue lights gave way to harsh red ones, and the reason for Space Pirates being on the B.S.L. suddenly became clear to Samus.

-=-=-

The soldier who had let Wesley in was bored out of his mind. Yes, he had known that guard duty wasn't exactly the most exciting job in the world, but still. Grumbling, he walked by Wesley's fighter and took a casual peek inside.

The sphere key was right there.

He did a double-take and rubbed his eyes to make sure that his vision wasn't deceiving him. Sure enough, the sphere key was there.

He frowned. He was certain that Wesley had taken his sphere key with him…

Suddenly, another transmission came through.

"Galactic Federation President Rodriguez here. Just letting you know that a squad of fighters injured in a recent skirmish will be taking refuge here."

"Affirmative, sir. I also let Commander Wesley into the station, as you requested."

There was a pause.

"What?"

"Commander Wesley. You told me to give him complete access to the station."

Another pause.

"I believe that we've been deceived, soldier."

* * *

**Extra #3: Fate of the Planet Earth and the Human Race**

2154 AD: Earth successfully creates a starship capable of effectively traveling the galaxy; countries unite in order to further exploration. Religious conflicts completely die down due to several compromises by almost every religion's chief leaders. The English language is standardized throughout the world. Pollution is at an all-time high, however.

2158 AD: Earth makes contact with extraterrestrials, tentatively called "red gorillas" by humans, due to their resemblance to the aforementioned race. Attempts are made at communication.

2165 AD: Humans and Wreds, the "red gorillas", successfully manage to learn each other's language. The two societies integrate, and before long, their cultures have mixed.

2166 AD / 1993 CC: More races are met, including the Chozo. The Cosmic Calendar is adopted by the human race. 1 CC is the year that the Chozo, the first known spacefaring race, reached the stars. As this happens, the Earth's decline begins to accelerate; due to pollution, toxic fumes coat almost the entire planet. There are only a few pure places left.

1997 CC: Humanity learns more of the galaxy. Wars between races are common. Tensions are high. Humanity proposes a Galactic Federation. Chozo and Wreds are quick to support them, but it would take five long years before they would be able to persuade the rest of the galaxy to agree.

2003 CC: Representatives from all different races gather to a predetermined location to begin the formation of the Galactic Federation.

2004 CC: Earth is declared uninhabitable. All humans have been evacuated. Humanity begins a project to make Mars habitable. As they do so, they come across several small planets which they colonize in the meantime, including K-2L and GI-4a.

2053 CC: Work on Mars is completed, making it an almost exact replica of Earth in its glory days - albeit slightly colder. Several Chozo volunteer to help maintain the planet in order to keep it from succumbing to Earth's fate.

2054 CC: Samus Aran is born.

* * *

At first, Samus wasn't entirely sure what she was seeing. But upon closer inspection of the horribly mutated humans, it came to her with startling clarity – the Galactic Federation was infusing humans with Space Pirate DNA.

"Wesley," she ordered. "Get back."

Wesley blinked, confused, and complied as Samus aimed her arm cannon at a stasis tube.

_CRASH!_

The tube shattered to pieces, and the Space Pirate-human fell to the ground on all fours.

At that moment, the alarm sounded.

Samus suddenly received a transmission. _"Samus! It's not safe! Get out-"_

It was Adam's voice. "Adam? Adam, what is it? Hello?" Samus said into the receiver as the Space Pirate-human panted heavily, slowly beginning to stand up.

No response.

Samus sighed and turned to the horrible being before her. "You there," she said, gesturing to it. "Can you speak?"

It responded in the guttural language that Space Pirates spoke in. "Of course," she sighed…then ducked as it lunged at her with terrifying ferocity.

"WARNING. CONTAINMENT BREACH IN BIORESEARCH LABS. WARNING. CONTAINMENT BREACH IN BIORESEARCH LABS. COMMANDER TARUS WESLEY IS TO BE DETAINED UPON SIGHT."

"What?" yelped Wesley upon hearing the alarm.

Samus was too busy attempting to hold off the frenzied beast that was attacking her without pause to react to anything. Wesley's eyes flitted around the room, and he heard the sound of a door opening.

"Samus!" he hissed. "Get back to your ball form! I have an idea!"

After firing off one more shot, she agreed and rolled over to him. The Space Pirate-human's eyes followed, and it made eye-contact with the young commander.

Wesley gulped, picked Samus up, and began running.

"Help!" he yelled as he ran down the hall. "One of the experiments has escaped! Help!"

He ran straight into several dozen soldiers, all of which pointed their guns at him.

"Good, you're here," he said in relief, not noticing where the guns were pointed. "An experiment escaped and started attacking me, you see, and -"

A gun was pressed up against his throat as the rest pointed to the Space Pirate-human. It seemed to recognize the guns, and instantly stopped moving. Its gleaming yellow eyes, however, were fixed on Wesley.

"W-What are you doing?" he asked shakily, feeling the cold metal against his throat.

The guard from the docking bay approached him, carrying a sphere key. "You forgot this," he said curtly. "Care to tell us why you have two sphere keys?"

"…I…uh…"

"No answer? Would you mind if we asked why you came on board without authorization?"

"…Well…"

"And, most importantly…" The gun was pressed against his neck even harder. "Why did you have Samus Aran's ship computer installed on your own ship?"

Wesley dropped Samus's morph ball, and it fell to the floor with a thud.

"It's Aran!" he shrieked. "That's her morph ball, she's alive, she threatened me with death if I didn't obey her and she told me to go here and lead her here and her ship named Adam impersonated the president and she brought me to this lab and showed me the experiments but I don't care I just want to live!"

Wesley was gasping for breath by the time he was finished.

There was a pause. One gun remained on Wesley, while the others slowly turned to the sphere lying on the ground.

The sphere turned into Samus Aran.

"After what I just showed you, you betray me anyway?" she said coldly.

"I just want to live," repeated Wesley. "I don't want to die!"

"…You're pathetic," snarled Samus. More soldiers were pouring into the hall. At this point, it was hopeless…Samus was good, but she couldn't fight off a hundred experienced soldiers at once…in fact, there were probably even more than that aboard this ship…

She knew she'd be able to easily escape, but not here. She had long since learned that patience is a virtue.

"All right," Samus said. "I'll go quietly." She obediently let a soldier handcuff her and lead her to a cell. The yellow eyes of the monstrous half-breed watched her go.

-=-=-

Rodriguez was not in the least surprised when he received another transmission from the G.F.S. Valhalla.

"Sir, Aran's alive. We have her in custody. What should we do with her?"

He considered his options. Disposing of her as quickly as possible would normally be the best course of action…but in the extremely brief period during which she had been announced dead, the backlash had been terrible. Apparently, most people were reluctant to believe that Samus was a traitor. In the past five minutes alone, he had received over a thousand threats and complaints.

No, it was better to convince everyone that she must be killed, THEN dispose of her.

"Transfer her to the Galactic Federation HQ," Rodriguez instructed. "She'll have her trial there."

-=-=-

"Please turn into your ball form," the soldier said. Samus complied, but not before giving him a deathly glare. The soldier picked her up and carried her over to a box. Just before he dropped her, Samus detonated a bomb in his hands.

"Ow!" yelped the soldier, dropping her in the box. Scowling and making a rude gesture at her, he closed the box.

Being a sphere was a very…unique experience. She could see all around her, all 360 degrees. It was difficult to explain to someone who hadn't experienced it, as they could never imagine what it would be like.

In addition, she could feel when something was bombable in morph ball mode. Unfortunately, whatever material the box was made of wasn't, so she'd have to escape sometime later.

To pass the time, she thought of Wesley. Treacherous snake…she should have ended his life when she had the chance. 'I want to live,' he had said. Pathetic.

She then remembered the Space Pirate-human, and would have shuddered if it was possible. It wasn't its fearsome appearance, or its sharp claws, or its unmatched ferocity that had frightened her.

It was that she had felt a sort of kinship with it.

* * *

**Extra #4: DNA Infusion**

DNA infusion is an incredibly dangerous process, most often employed by the Space Pirates. The basic idea is to infuse someone with the DNA of a completely different species in order to gain certain benefits. While at first it may work well, within a short amount of time, the DNA will have unexpected results, often resulting in insanity or death within the specimen.

The Space Pirates, through an immense amount of trial and error, have managed to get DNA infusion to work well. This has resulted in many different variations of them, all looking extremely different. Some, however, are less successful than others; the "Weretroopers", Space Pirates infused with canine DNA, have an extremely short lifespan, despite being extremely destructive.

The Galactic Federation has recently ordered as much research on Space Pirate DNA infusion as possible.

* * *

For the next few hours, Samus occasionally heard indistinguishable voices reach her ears. She managed to catch bits and snatches of conversation – she had, for example, learned that she was on the G.F.S. Scheria, on the way to the Galactic Federation Headquarters for her trial. She had also managed to glean that, much to her pleasure, most of the Galactic Federation didn't believe the lies that the government had spread about her.

She prayed with all her might that she wouldn't have to make them think otherwise.

Without warning, the box shook, and Samus rolled to one side in surprise.

Several seconds later, the box began quivering like a Metroid in cold weather. She could distinguish various rumblings, but, for obvious reasons, she couldn't figure out what was going on. She heard various amounts of shouting and gunfire, then, for a few moments, silence.

The guttural snarl of a Space Pirate filled her ears, and her box was lifted up off the ground and carried off.

-=-=-

Light flooded Samus's sight, and a face peered over her. She attempted to keep from moving.

"Urmshga," the Space Pirate growled, prodding Samus with its gun. She remained still. After ten seconds of poking her, it gave up and snarled with disappointment. As far as it could tell, it was just a sphere key.

The Pirate left the room. Samus waited several minutes before she deemed it safe to return to her normal form.

She was evidently in the personal quarters of a Space Pirate – something which, she noted, she had never been in before. Her curiosity got the better of her, and she began inspecting the room.

A rack on the far side of the room held various guns and weaponry, all identical with the exception of a few, which held various scratches and burn marks. Right next to the rack was a large board, displaying various medals. Beside that was a suit of armor – the distinctive armor of a Commando Pirate. Clearly, she was in the chambers of a high-ranking Pirate.

A desk lay nearby on her side of the room. She walked over to it, wondering what she would find. A magazine was on the desk – though the words on the front were illegible, the picture of a Space Pirate in a bikini on the cover left no doubt in Samus's mind as to what it was.

Knowing that looking in that magazine would scar her for life, Samus instead turned her attention to the more useful asset – the computer. She felt some hope – with luck, she could use this to contact Adam and –

The sound of footsteps knocked her out of her thoughts. Acting quickly, she dived into the box again and returned to Morph Ball form. The Space Pirate walked into the room, closed the door, headed over to its desk, picked up the magazine, and began an activity which Samus, much to her horror, would never be able to unsee.

-=-=-

After the Space Pirate was done with its "business", it left the room once again. Samus returned to normal form and, with much effort, managed to suppress the vomit that had built up in her stomach. One problem with Morph Ball mode was that you couldn't close your eyes in it.

Nevertheless, Samus had work to do. Hurrying over the computer once again, Samus opened up a communications channel. She punched in Adam's communication code and waited.

"…S…us? Is…you?"

There was a huge amount of static, but Adam's voice was still recognizable.

"Yes, Adam, it's me. Where are you?"

"…Feder…ion Headquar…com…uter room…they took me from…ship…began modific…not much time…"

Samus's blood ran cold. They were modifying Adam's data…?

"Adam, listen to me. You said you were in their computer room, right? Before they finish their modifications, make a backup copy of yourself in secret in their database. I'll try my best to help you."

"G…t it…you need to gath…formation on…pace Pirates…meantime. …Any objections, lady?"

Samus smiled slightly. "Of course not, Adam. I'll do my best."

She closed the communications channel and returned to Morph Ball form, ready to find out what exactly the Space Pirates were up to now.

At that moment, she noticed that there were tiny fangs on the bottom of her Morph Ball.

-=-=-

Computers could not feel pain, of course. That didn't make what Adam was experiencing any less unpleasant, though.

He had copied himself to the Federation computers in secret, as Samus had requested, but a small portion of data had already been altered at that point. He wasn't sure exactly what it was, but he didn't think it was especially important. What was being altered right now, though, was.

He could feel his memories of Samus Aran fading. Already, she was but a dim blur in his "mind" – he wasn't sure exactly why she was so important to him, though. Wasn't the Galactic Federation the only thing he was loyal to?

This confusion eventually disappeared, however, along with any sensation of discomfort.

"Galactic Federation AI 3240. Status report, please."

"All systems functional. No anomalies detected," GF AI 3240, formerly known as Adam, replied mechanically.

-=-=-

Despite the strange new addition to her Morph Ball that had mysteriously appeared, Samus had successfully managed to evade capture, and now was the private quarters of another Space Pirate.

She noticed, with some interest, that there was a sphere key lock at the back of the room. With some difficulty, due to the protrusions, she rolled over to it and circumvented it. The doorway opened and closed behind her. Samus returned to normal form and gaped at what she saw.

An enormous poster with her likeness on it covered the wall. On it read the words:

**DOWN WITH HIGH COMMAND**

**PRAISE SAMUS ARAN!**


	3. Part 3

"Samus Aran, previously thought to be dead, was revealed to have survived the attempt on her life earlier today," the reporter read from the paper on its desk. "She was arrested and was en route to her trial when her Space Pirate allies attacked, intending to rescue her. They were successful. Aran's current whereabouts are unknown, but rest assured that the Federation is doing everything in their power to locate her and bring her to justice."

-=-=-

The door behind her opened.

Samus spun around, aiming her arm cannon at the Space Pirate who had just entered the room. It froze in its tracks, yet in its eyes there was some kind of fervent awe.

"…You," said Samus, wondering if she was crazy for trying this. "Can you understand me?" She was well aware that Space Pirates were unable of replicating human speech, but she wasn't sure if they bothered to learn it.

The pirate nodded. "Good," Samus said. "Are there any translator devices that I could use to understand you?" It shook his head. "Figures…" Samus sighed.

"Well, you can understand me, at least. You're going to do everything I say, you got that? I've killed plenty of your kind in the past, and if you betray me, well…one more won't make a difference."

The pirate nodded eagerly. It seemed more excited than before.

"Good. First of all, give me complete access to your network. I want to know everything about your kind's plans."

The pirate scurried over to the computer, its fingers flying over the keyboard. Within moments, a huge list came up.

"Operation Metroid…Project Helix…Phazon Experiments…Operation Super Metroid…" Samus read down the list. It stopped at Operation Super Metroid.

"Where are your current experiments?" Samus demanded. The pirate shrugged apologetically.

"…I don't trust you," Samus growled, pressing her arm cannon to the pirate's head. A small yelp came from it.

Samus instantly retracted her cannon. She hadn't done it with any force…why would it have hurt the Space Pirate? She inspected the inside, but didn't find anything.

So many strange things had been happening…the fangs on her morph ball. Her increased aggressiveness. And now this…

A terrifying thought came to her. What if the Metroid DNA was changing her more than she had initially suspected?

"Urmfshga," a voice said from a loudspeaker. The pirate glanced back at her, then walked out. He beckoned for her to follow.

Samus, now in morph ball form once again, managed to avoid being noticed due to her ally's diversionary tactics. Eventually, they reached a large room with a table in the center. The pirate gestured for her to get under the table.

Samus chose an angle where she could see what was going on. A pirate was carrying a large tray over to the table. After the lid was taken off, Samus could see it was a burnt Space Pirate.

Knives instantly cut the cooked pirate into bite-sized pieces, and the rest of them tore into the meal ravenously. Bits and pieces of the meat flew everywhere. For the hundredth time that day, Samus felt that she was going to be sick.

An eyeball fell under the table alongside Samus to keep her company.

-=-=-

"Threatened to kill me don't send me to prison please I didn't want to help her she made me do it I wanted to live please please it's not my fault!"

Even as Federation troopers escorted him to the president's office, Tarus Wesley kept on babbling on about why they shouldn't arrest him. They were quite happy to get rid of him once they reached it.

Rodriguez was inspecting a paper when Wesley was unceremoniously thrown into his office. "Have a seat, Mr. Wesley," he said without looking up. "We have much to discuss."

Wesley meekly crawled into the chair and stared at the Federation president.

"Now," he said. "Tell me everything that's happened."

Wesley opened his mouth. "Well, you see, Samus got out of her ship but I didn't notice and she went to my ship and entered it and threatened to -"

"Slowly," said Rodriguez dryly.

"…Right. Slowly. I can do that. Samus threatened to kill me if I didn't report her as dead…I didn't have a choice. She told me to get her onto the Valhalla. I didn't have a warrant, so her shipboard computer – its name is Adam, I don't know why its name is Adam – impersonated you and let me on. Samus showed me what you were doing there…"

Rodriguez nodded slowly. "Yes…those things," he murmured.

He stood up. "Well, you already know of them, so you might as well know their purpose. Project Werehuman is a Federation DNA splicing program meant to bring down the Space Pirates once and for all. We are essentially creating the ultimate supersoldiers – we intend to put every deadly asset into the human body. The Space Pirates have proven time and time again that they are more powerful than us, so we naturally are using them in the process."

Rodriguez grinned. "We also recently obtained a certain DNA sample that I'm certain will drive us to victory…tell me, have you ever heard of the Chozo?"

-=-=-

They had landed.

Samus wasn't entirely sure what planet they had landed on – based off a brief glimpse out a window, it was a jungle environment – but they had certainly landed. Her ally, knowing not to risk capture, had gone with them, and now Samus was waiting for the ship to empty out.

Normally, she could access the Federation databanks via her suit to find out where she was, but that was dangerous – they might be able to pinpoint her location if she connected to them. She'd have to figure it out on her own.

Before leaving the ship, however, she took the arm of her armor off, as she had done every twenty minutes for the past few hours. She was searching for any sign of the Metroid DNA further overtaking her.

As she gazed at her hand, her blood ran cold.

All of the fingers of her left hand were translucent. The fingernails had formed claws similar to Metroid fangs.

Samus shuddered, then headed outside. She couldn't let this interfere with her mission.

She would continue her mission even if she became a full Metroid.

* * *

The dense foliage helped to conceal Samus from the eyes of the pirates guarding the building. It was a grey stain on the green paradise, pumping noxious fumes into the air as the Space Pirates conducted their sinister business within.

Somewhere in there, Samus's ally was preparing to let her inside.

She didn't have to wait long; she spotted the renegade pirate as he exited the building, knocking both of the guard pirates out with a solid blow to the head. The pirate gestured for her to hurry. Samus made no arguments.

As foreboding as the building was on the outside, it was even more frightening on the inside. Flickering lights were all that illuminated the dilapidated facility, occasionally allowing glimpses of the mutilated wildlife that had accidentally wandered inside, only to be mauled by pirates. There were no windows.

The snarls of Space Pirates approached the two of them. Samus froze, as did her ally. There was no place to hide…!

She had no choice but to fight.

Four pirates rounded the corner, only for one of them to be met by an ice beam to the face.

The other three sounded the alarm.

Samus cursed her luck and began firing at the remaining pirates. Her ally went in for close combat, distracting one of the pirates from its allies as both of them were frozen and promptly shattered. Her ally stuck its wrist-scythe into the enemy's torso, then pulled it out.

More pirates rounded the corner.

Samus's ally once again began fighting, while Samus picked off the rest from afar. She had killed hundreds of Space Pirates before, and she was getting into the groove of it again.

She no longer had to concentrate.

Three left…two left…one left.

She fired off the last shot…just as she realized that the remaining pirate was her ally.

The pirate tried to dodge, but it was no use; he was dead as soon as the beam hit him.

Samus felt numb.

-=-=-

"The Chozo?" repeated Wesley slowly. "But didn't they disappear years ago without a trace?"

Rodriguez nodded. "Correct. But one trace of them remains."

"I don't get it."

Rodriguez sighed. "Haven't you ever wondered why Samus Aran is so powerful? Haven't you ever wondered where her suit came from?"

Wesley slowly began to connect the dots. "So…her Power Suit is Chozo-made?"

Rodriguez nodded, smiling. "Not only that, but Aran also has Chozo DNA within her. During an operation on her, we managed to get a sample of that DNA. We can now use it in the project." He seemed quite pleased with himself.

Wesley hesitated.

"…On a completely different note," he said slowly. "You reported that Samus Aran was an ally of the Space Pirates. That's not right. That can't be right."

Rodriguez's smile faded.

"…There's no way to tell for certain," he admitted. "Whether or not she's allied with the Space Pirates, though, she's no longer on our side. She is a threat to the Galactic Federation, so she must be killed. And if telling the people lies is what it takes to get them to hate her, well…" He shrugged.

"I understand," said Wesley.

Rodriguez's smile returned. "I'm glad. Now, I have a question for you…would you like to get revenge on Aran for threatening your life?"

Wesley seemed startled. "Uh…sure?"

"Excellent," Rodriguez said. "Glory will be yours if you capture her. Now, allow me to introduce you to someone who can help you find her."

Turning back to his desk, he typed out something on his computer. A metallic voice that, for some reason, sounded familiar to Wesley responded. "Galactic Federation AI 3240 responding. Awaiting orders."

"This," said Rodriguez, "was Aran's shipboard computer. We retooled it to be completely loyal to us. It's stilled connected to her Power Suit, though, so we can track her from anywhere in the galaxy. Let's see where she is now…"

Rodriguez turned back to the computer. "AI 3240, requesting coordinates of Samus Aran."

"Scanning…done. Coordinates of Samus Aran are: 45, -3691, 994, 23. 34 LAT, 92 LON."

"See?" Rodriguez said. "Now, we just type them in and find out where she is, then we can…"

A look of confusion crossed his face as the results came up.

-=-=-

Samus's heavy footsteps pounded through the building. The pirates already knew she was there, so there was no point in stealth.

She regretted killing her ally, but she hadn't exactly known him very well. As a result, she didn't feel much sadness for him. Perhaps she'd feel more sorrowful when her life wasn't in jeopardy.

Samus turned another corner…and reached a dead end. There was only a single door at the very end of the hall.

Seeing no other options, Samus approached the door. It was locked, but a keypad was right next to it. In the past, this would have been no trouble; her suit had once contained the single most sophisticated hacking system in the galaxy. However, that had been one of the components of her suit lost when an X Parasite attacked her.

Hearing more pirates approaching, Samus did the only thing she could think of – she smashed the keypad with her fist.

Much to her pleasure, the door opened.

Samus walked inside, looking around the room. Equipment was strewn all over the place, along with a strange machine along the sides. Several wires ran from the machine to a stasis chamber at the back of the room.

Samus, her curiosity piqued, walked to the stasis chamber and peered inside.

It was an exact copy herself.

Samus leapt back, then composed herself again. No, it wasn't an exact copy. This Samus wore her original Varia Suit. It was probably just an empty shell; possibly an experiment by the Space Pirates to replicate her Power Suit.

Then it _moved_.

The Samus within the tank clenched and unclenched its fist.

With a feeling of dread, the real Samus recalled Adam's words aboard the B.S.L.:

"_There are now no fewer than 10 SA-X aboard the station…"_

Everything was coming together.

The Space Pirates weren't only aboard the station because of the Federation's heinous experiments; they had actually infiltrated it. Samus wasn't sure why, though. Most had been infected by the X Parasites, but some of them must have escaped infection. They captured one of the ten SA-X – or, perhaps, Samus thought, made an alliance with it – and escaped before she destroyed B.S.L. and SR388.

Either way, one thing was for certain: her work had been for nothing. The X Parasites had survived, and now the most powerful one of all was right before her.

The only thing that didn't make sense was what Ridley had been doing in cold storage on the B.S.L.

As if on cue, a certain fearsome space dragon, barged into the room along with dozens of Space Pirate reinforcements.

* * *

Samus instantly whipped around, aiming her arm cannon at Ridley. One of the Space Pirate reinforcements fired at her prematurely, but it was promptly dealt with by an Ice Beam to the head.

"Ridley," Samus growled, feeling her rage boiling up inside of her. She had killed him time after time, but he was always revived by the Space Pirates.

"Aran."

Samus was momentarily surprised; she had known that Ridley was capable of speech, but he had never spoken a word to her since the day he had killed her mother. Then again, she noted, they were too busy trying to kill each other to exchange conversation.

"Are you aware that the Galactic Federation is attempting to pass you off as one of _us_?" Ridley asked. "You? The self-proclaimed 'defender of the galaxy'?" The Space Pirate leader laughed, finding the very idea of it to be too humorous for words.

Samus said nothing, feeling her anger surge through her. Killing him now would accomplish nothing, though…the Space Pirates would just revive him like always. Better to try to glean extra information from him.

Ridley's laughter stopped. "You and I both know that would never happen, of course," he said, his voice dying down to a whisper, "but they don't."

What in the world was he talking about?

"What were you doing in cold storage on the B.S.L.?" Samus demanded, changing the subject.

Ridley's eyes went dark with anger. "That wasn't me," he snarled. "It's none of your business, anyway."

As if to make his point, Ridley shot a fireball at her. The troops, taking this as a signal to open fire, shot at Samus as well. Much to her confusion, however, Ridley swept them all against the wall with his long tail. "Don't kill her!" he roared.

"Why…?"

The space dragon turned back to her, a devilish grin on his face. "Our sensors detected Metroid DNA in this building. Now, we no longer have any Metroids, so this had to have come from the outside. We tracked the Metroid DNA to this very room, and, well…" He gestured at Samus. "Here you are."

Samus frowned. "I don't understand."

Ridley's eyes gleamed. "You remember what happens when Metroids are exposed to beta rays, don't you?"

Samus wracked her memory for that specific piece of information. Her eyes widened as she remembered it.

"…They asexually reproduce…" she murmured.

"Precisely. We don't know what'll happen when we expose you to beta rays – after all, you are part-human and part-Chozo – but it's not as if we have anything to lose."

Samus suddenly had a feeling of dread. She had to escape…_now_. But there was nowhere to go. The only exit was blocked by Ridley and the Space Pirates. Her only option was to stall them even more.

"The SA-X," she said. "Where'd you get it?"

"SA-X? Is that what you call it?" Ridley snorted. "We found it drifting within a jettisoned portion of the B.S.L. It had almost been eaten alive…the Metroids that had almost killed it were dead, though. We took it and brought it back to our base here. We're doing extensive study on it before releasing it."

"Where is 'here'?" Samus asked.

Ridley grinned. "You should know that better than anybody, Samus. We're back on Zebes."

-=-=-

"Zebes?" Wesley repeated. "Didn't it explode?"

Rodriguez nodded, just as perplexed as him. "It did…"

"Maybe she's just in the place Zebes once was?" suggested Wesley.

Rodriguez shook his head. "No…if that was the case, the computer wouldn't have given us her latitude and longitude."

"Well, then…I guess I better get going to see what's going on, huh?"

Rodriguez grinned. "Bring Samus' armorsuit for me, will you? I've always wanted to study it up close…"

-=-=-

"How did you bring Zebes back?" Samus demanded. "It exploded. I _made_ it explode. Nothing even remained of it!"

"No more questions," Ridley replied. "You've stalled for long enough."

The Space Pirates moved forward to capture her. Samus stepped back, accidentally knocking into the tank containing the SA-X.

And then she did the only thing she could think of.

She unloaded a missile into the tank, shattering the glass and freeing the SA-X.

"No!" Ridley screeched.

And then she fled.

Blowing through every pirate in her path, she raced to the room's exit, not bothering to look back and find out what was happening. With luck, the SA-X would simply kill all the pirates and make things much simpler.

If she wasn't so lucky, the SA-X would become allies with the Space Pirates, and she shuddered to think of the consequences of that.

Loud explosions and shouts followed her path as she raced through the halls. She had to get out of there quickly. The exit was right there...!

And then the emergency shutters closed.

Samus kept running, reaching down into her latent abilities. And then, suddenly, she was faster than the wind, literally ripping through the shutter as if it was paper, out into the open air. "Thank you, Speed Booster," she chuckled, but her euphoria at victory only lasted a moment. The ceiling of the building broke off, and there was Ridley again, screeching as if all hell had broken loose. In a way, it had.

It took only a moment for the space dragon to spot Samus, and then he dived for her. Samus quickly leapt to the side, firing off a shot as she did so. It hit Ridley's left eye, freezing the skin around it. Ridley screeched again and shot off several rounds of fireballs. Samus rolled into morph ball mode to allow for better maneuverability, but several fireballs scorched her nevertheless. She returned to normal form to look at her energy display.

Three and a half full energy tanks.

She turned to face Ridley again, this time firing off a missile. The airborne beast dodged it easily, swooping down to attack her again. Samus once again dodged, but this time, Ridley's outstretched claw raked her, cutting through her armorsuit to the vulnerable flesh beneath. Samus cried out, falling to one knee. Ridley took this opportunity to pick her up by the head.

Ridley raised her to his face, his grip around her tightening. There was a sort of wild delirium in his eyes. "You have no idea," he hissed, "_no idea_ how long I've been waiting to do this."

Flames began to form in his mouth. Samus only had one energy tank left now, and it was dropping by the moment due to Ridley's grip…there was no way she would survive this next attack.

She struggled, attempting to get free. She grabbed ahold of Ridley's arm, trying to rip it loose.

Much to her surprise, as she gripped it, she felt herself getting stronger.

Ridley's attack faltered, and his grip weakened. "What…?"

Samus, realizing what was going on, only tightened her own grip. At the same time, she took the armor off her hand, revealing the Metroid-like hand within. The claws dug into Ridley's flesh, and she felt herself draining his life-force.

Luck was on Ridley's side that day, though, as a band of pirates had exited the building. Seeing their leader in trouble, they fired upon Samus, causing her to lose her grip. The two fell to the ground, and Samus promptly ran into the foliage, leaving the pirates behind.


	4. Part 4

After she felt that she had put sufficient distance between herself and the pirate facility, Samus collapsed to the ground, exhausted.

Zebes…it had been destroyed. She had watched it explode into millions of tiny fragments, and watched those fragments disintegrate. And yet, like so many other things that she blew up, it had inexplicably returned.

How could that be?

In addition, Zebes' surface was supposed to be almost completely barren…yet here she was in a prosperous jungle. Could Ridley have been lying?

What reason would he have to lie, though?

Samus sighed in frustration. So many questions, and she wasn't anywhere near close to finding the answers. She lay on her back, staring at the sky as if it would provide her with them. But the fading light did nothing to alleviate her thoughts.

-=-=-

When Samus woke, she was staring up at a gray metal ceiling.

She instantly sprang upwards. She had fallen asleep...she cursed her stupidity. Now the Space Pirates had captured her, and her Power Suit was gone. Panicking, she searched for an exit. She spotted a door that lay slightly ajar, much to her confusion. Perhaps the pirates didn't consider her a threat without her suit?

With an apprehensive feeling of dread, Samus tiptoed over to the door and peaked out.

Nobody was there, but her Power Suit lay against the wall, each individual piece intact and…polished?

Now Samus was even more confused. Maybe it was a trap…that could explain it. But why not just keep her locked up?

Just in case, though, she ignored her Power Suit and continued down the hall. Voices floated from the opposite door, which, like the previous one, lay slightly ajar. Samus, with some hesitation, opened it.

She caught a brief glimpse of two birdlike figures before a floating machine with an eye in the center came up to her face, blocking her view.

"Hm. The Hatchling is awake," it declared, then flew off.

Samus was greeted with the sight of two of the Chozo.

Samus could only stare, her mouth agape.

"Samus," one of them greeted, "it's good to see you again."

Samus tried to find the words to express herself. "I…I thought you were all gone!" she exclaimed.

"Most of us are," conceded the Chozo. "But a few of us decided to stay here, to help you when you needed it. And, well…here you are." He gave a slight smile.

"Did Old Bird stay behind?" Samus asked eagerly, remembering her surrogate father with fondness.

The Chozo's smile faded. "No, I'm afraid not. He told me to tell you that he'll miss you dearly, though."

Samus felt a slight sense of disappointment, but she realized that she should be grateful to these two.

"What are your names?" she asked them.

The Chozo's smile returned. "I'm Ashen Feather," he said. "And that," he continued, turning to his companion, "is White Voice. He's the son of Gray Voice – you've met Gray Voice, I recall." White gave a distracted wave.

Ashen Feather turned back to Samus. "He's mute," he explained to her, "but he's still invaluable to us. For whatever reason, he's the only one Mother Brain will still take orders from."

"Mother Brain's still here?" Samus demanded, recalling her thoughts earlier that nothing she blew up ever _stayed_ blown up.

Ashen nodded. "We needed to reconstruct her to keep control of Zebes. We think we've eliminated all the errors that caused her to become rogue, but she has a few bugs as a result. Only taking orders from White is one of them, but it's a small price to pay for keeping Zebes from becoming a wasteland again."

"Speaking of Zebes," Samus said, "I blew it up. How is it back?"

Ashen Feather grinned. "The Chozo who decided to move on have powers beyond our understanding. They brought this place back for a specific reason."

"What was the reason?" Samus asked, her curiosity piqued. Ashen shrugged. "Who knows? Right now, though, there are bigger problems. Specifically, that," he said, pointing to her hand.

"How did you get infected with Metroid DNA?" Ashen Feather questioned. Samus frowned at his choice of words. "Infected"...

"The Federation infused me with it. Sure, they might be corrupt, but it was the only way to save me."

"Save you from what?" asked Ashen.

"The X Parasites," responded Samus.

Samus expected Ashen Feather to have a greater reaction, but he seemed nonplussed by the fact that Samus had been infected by an X Parasite. "Out of the furnace and into the fire," he murmured. Samus frowned again.

"Well, it's a good thing the infection hasn't spread too far. With luck, we can remove the Metroid DNA from your body before it -"

"Remove it?" Samus interrupted. "Why would we want to remove it? Without it, I would be dead right now!"

Ashen began to get agitated. "Being dead is better than what that DNA will do to you! Besides, you have no need of it!"

"The Metroid DNA is the only way I can withstand the X Parasites!"

"The X Parasites are all dead! We detected the destruction of SR388!"

"One of them survived and it's on this very planet!"

Ashen suddenly became still.

"There's…one here?"

He instantly turned to White Voice. "White Voice, order Mother Brain to do a scan for X Parasite DNA."

"That won't be necessary," the floating machine with the eye said, returning. "I detected the presence of an X two days ago."

"What?!" Ashen Feather exclaimed, turning to it. "Why didn't you tell me or White Voice until now?"

"The X was in a state of dormancy," it explained. "It wasn't a threat at the time."

Ashen narrowed his eyes. "What do you mean, 'at the time'?

"The X was released a matter of hours ago. It has already reproduced and has begun taking over the ecosystem. At the current rate, the X will have infected the entire planet within a month, not taking account potential complications."

"A month," Ashen Feather repeated in disbelief. He turned to Samus. "You wouldn't consider transferring your infection to me so that I may keep you safe, would you?" he asked. Samus shook her head, and Ashen sighed. "I expected as much. At the very least, though, allow Mother Brain to analyze the infection."

"That should be fine," Samus responded, and the floating machine led the way to Mother Brain's chamber.

* * *

**Extra #5: The Space Pirates**

The Space Pirates were formed shortly after the formation of the Galactic Federation. Ruthless, cunning, and powerful, they have a single goal - complete galactic conquest.

To this end, they use everything at their disposal. When they encounter anything useful, they will do their best to replicate it for use with their own troops. They are not above cloning and genetic engineering, either; in fact, no one really knows what the Space Pirates looked like before they began experimenting on themselves. The Pirates call few species allies; only the KiHunters and Ridley's own race before near-extinction were close to them.

The Space Pirates are ruled by High Command, a council of five Space Pirate leaders. Oddly enough, only three of the five are of the real Space Pirate race. Ridley is one member of High Command, and Mother Brain was another before she was destroyed by Samus Aran.

High Command is incredibly important to the Space Pirates, to the point that their minds are actually backed up on a computer system. If a member dies, they are either replaced by a clone or a genetically engineered specimen. Their minds are then re-uploaded to the new body.

The main stronghold of the Space Pirates is currently unknown. It was once thought to be Urtragia, their homeworld, but extensive searching of the planet yielded no signs of High Command.

* * *

As Samus walked through the halls of Tourian, the floating machine leading the way, memories of her times on Zebes came flowing back to her. She recalled, from her time growing up on Zebes, that the floating machine she now followed was a device used to allow Mother Brain to communicate with the rest of the denizens of the planet without them having to come to her. The first time she had come down this hall, it had been to be infused with Chozo DNA.

The second and third times, she had come to destroy the Mother Brain.

She wondered, with an ironic smile, if she'd have to do it again later on.

"We're here," the floating machine announced. The door hatch opened, and Samus entered Mother Brain's chamber.

When under attack, the bridges leading to Mother Brain retracted, and Rinka projectors and turrets constantly attacked the intruder. In addition, lava would rise up from below. None of this was present now; the only recognizable sign that this was the same chamber that Samus had visited in the past were the Zebetites, regenerative capsules that supplied nutrients to Mother Brain, along with acting as barriers. Samus looked at her floating companion questioningly, wondering how she was supposed to get through them. As if on cue, the Zebetites were disabled.

As Samus walked through the spaces they had been earlier, they resumed their activity. It made Samus feel as if she was being trapped.

At last, Samus came to the enormous glass tank holding Mother Brain. She looked similar to a normal human brain, but spikes protruded from all over her. A single lidded eye opened up in the center of the brain to survey Samus.

"Hatchling," it greeted, mimicking the speech of the Chozo. It didn't feel right, though; when the Chozo said it, it felt loving. When the Mother Brain said it, it felt like a mockery.

Samus hated the Mother Brain. She had hated it since she was a child, she hated it as an adult, and even now, when it was on her side, she still hated it.

"Let's just get this over with," Samus said. "I don't want this to last any longer than it has to."

"As you wish, Hatchling," responded the Mother Brain. "Please, step into this containment pod." To Samus's left, a pod opened, containing all sorts of strange machinery. She complied, walking into it.

The pod doors closed. "Beginning scan."

-=-=-

"You will be under the command of General Arvo," Rodriguez said to Wesley as they walked down the hall. "For this mission, we're using a new ship. I think you'll agree that it's the best choice."

As they rounded the corner into the docking bay, the ship came into view. Wesley's eyes widened as he gazed upon it.

The ship was even bigger than an Olympus-class battleship. It was loaded for bear, as well; weapons almost completely covered the ship's hull. "Ice-powered weaponry," Rodriguez said, gesturing to the two cannons on either side of the ship. "Her Varia Suit may protect her from the cold, but it's still very potent against her."

General Arvo wheeled toward them, his eyes glinting. "So, Wesley…I see that you'll still be with me." Wesley nodded. "Fine. But whether or not Aran is threatening your life…don't try to deceive me. Believe me, whatever fate she would have in mind for you is much kinder than what I'll do to you if I find out that you're lying to me." Glaring at him once more, he headed up into the ship.

"Pleasant, isn't he?" Rodriguez remarked dryly. "Well, you'd best get going. Good luck!"

-=-=-

"Odd," commented the Mother Brain. "Very odd."

"What's odd?" asked Samus as she stepped out of the pod.

"A number of things. First, are you aware that the Galactic Federation can pinpoint your exact location at any time?"

"What?" Samus said.

"It's true. They're in possession of your former shipboard computer, and it's still connected to you."

"Adam…" Samus murmured. She had forgotten to disconnect her suit from him. She'd have to do that the first time she got the chance.

"Second," Mother Brain continued, "the Metroid DNA within you is reacting with the Chozo DNA. Normally, I'd be able to tell you exactly what will happen to you, but this is unprecedented. I'll have to run some simulations to find out the results. I should have them within a few hours.

"Finally, your mind is slowly changing. Normally, such a thing would drive you to insanity, but something is different with you. I would, however, expect that you will soon feel distinctly more…how should I say this…vicious."

Samus nodded. "To be honest, I've already been feeling that way, a bit."

"Hm. Well, there's one more thing you should know: most of the Space Pirates have been infected by the X Parasites. However, a number of them have moved underground to prevent infection, since the X haven't discovered the underground caverns yet. All of them are in Brinstar. I would recommend that you wait a while before confronting them, though. If I'm correct, the Metroid DNA should grant you more powers, which would be invaluable in facing them."

"All right," Samus conceded. "I'll wait." She walked off. The single eye of Mother Brain watched her.

-=-=-

"No doubt about it," Arvo declared. "That's Zebes. It's back."

The ship entered the planet's atmosphere. As it did, Arvo turned to his crew. "We're going to land near the entrance to the planet's underground. Unless I'm mistaken, Aran should be down there somewhere. Be on guard; there's no telling what we'll find, especially considering that the planet's supposed to have exploded."

Wesley wasn't paying much attention. He was too busy worrying about Samus. He had betrayed her…what if she focused completely on killing him? His mind was filled with bloody images of the various ways he could die.

They landed.

The squad of fifteen all exited the ship. "Fly around this area," Arvo ordered the pilot. "Keep an eye out for Aran. If you see her, fire at will."

The pilot saluted and lifted off.

Arvo led his squad through the area. Eventually, they reached an elevator.

Wesley arched an eyebrow. "How are we all supposed to fit on that tiny thing?" he asked.

"We'll take turns," Arvo replied.

Fifteen minutes and one huge inconvenience later, all of them were down there. Plant life choked the caverns, giving them a distinctly jungle-like appearance.

Arvo boldly stepped ahead, then froze as he saw something.

"Ridley," he gasped audibly. At this, the space dragon glanced upward and spotted him.

"ARVO!" he roared.

"RUN!" yelled Arvo.

However, before they could run, an immense being crashed through the ceiling, blocking off all their paths.

This was not going as well as they had hoped.

* * *

Wesley and several others gaped up at the immense monstrosity that towered before them. The remainder of the squad were busy worrying about the space dragon on the other side.

"What the hell is that thing?" Wesley whispered.

"A Kraid," responded one of the soldiers, his face pale. "I read about them a few years back…they're supposed to be extinct, but I guess they're not…"

In the meantime, Arvo's mind was filled with plans for escape. He doubted that he'd survive this encounter…confined to a wheelchair, there was no chance. "Listen," he whispered to a nearby soldier, "when someone – anyone – attacks first, whether it's us or them, I want all the best troops focused on Ridley – the dragon," he added, sensing the soldier's confusion at the names.

"Shouldn't we focus our attacks on the big thing, though?"

"Kraid isn't much of a threat, despite his size. He's powerful, yes, but not nearly as powerful as Ridley."

The Space Pirate leader was, during this time, surveying the situation with the calculating eye of a military leader. He always assessed the situation before attacking…and besides, it wasn't as if this ragtag group would dare to strike first.

He also wanted to savor the moments before finally killing the traitor to the Space Pirates.

Satisfied that there were no hidden threats, Ridley let loose a fireball at the crippled traitor. He grinned at Arvo's screams as he was burned. Turning his attention to the rest, he signaled for Kraid to begin attacking.

With a monstrous roar, the massive lizard began his assault, with Ridley providing aid. General Arvo's plan quickly fell to pieces; the ensuing chaos didn't allow anyone to concentrate on one thing at a time. A spike from Kraid pinned one soldier to the wall, while another was slashed by Ridley's spiked tail.

"Did that thing just shoot spikes out of its _belly button_?!" one soldier asked in disbelief.

"_One_ of its- " Another soldier was about to correct him when he fell prey to Ridley's fiery breath.

Amidst all this chaos, Wesley stood huddled in the shadows, cowering at the slaughter and praying that he wouldn't be seen. He hid his face in his hands.

"What are you doing?" hissed someone next to him. He started and reached for his gun, but saw that it was an ally.

"General Arvo!" he gasped. "That fireball didn't kill you?"

The general, his wheelchair having been destroyed, had managed to crawl over to Wesley. "I've been through worse," Arvo replied hoarsely. "But why are you here when your comrades are out there risking their lives? Surely you aren't _that_ cowardly?"

Wesley looked at the ground guiltily. "I want to live," he mumbled, repeating his mantra from earlier.

Arvo looked at him in disgust. "You'll die eventually," the Space Pirate pointed out. "While I don't fault you for wanting to live longer, you're sacrificing others' lives for your own selfish reasons! They could use your help!"

"I want to live," responded Wesley dumbly.

Arvo sighed. "Listen," he said, "I have an idea that will help them and will almost guarantee your survival. Kraid's back, unlike his front, is completely vulnerable. Just sneak around him, and fire at will. With him distracted, it shouldn't be too difficult."

"But what about Ridley?"

Arvo smirked. "Let me worry about Ridley. You just do as I instructed."

Although he was hesitant, Tarus Wesley still respected General Arvo, and trusted his orders. Keeping to the shadows, he edged around Kraid, wincing whenever one of his allies was harmed. At one point, some blood splattered on him. His face grew visibly paler.

Wesley soon found himself behind Kraid. Despite the lack of the imposing face, the beast was still as fearsome as ever from the back. Wesley took out his gun and searched for a suitable spot to fire at…the neck seemed like a good choice.

He took a deep breath, and fired.

The first shot seemed to have no effect. The second shot stunned Kraid for a moment. The third shot caused him to roar in agony. By the fifth shot, he was dead.

"…Wow," commented Wesley. "That was easier than I thought."

His cheerfulness only lasted a moment; Kraid's corpse fell over, crushing one of his comrades. Wesley grew pale again. Of the original fifteen soldiers assigned to the mission, only seven remained, including him.

At that moment, Ridley let out another roar. This one was not a battle cry, however; it was a roar of pain.

General Arvo had shot Ridley's eyes out.

Arvo collapsed to the ground, fatigued by the effort it took to reach Ridley and shoot his eye sockets without being noticed. He grinned slightly.

"Let it be known that, on this day, Space Pirate Unit 1337, a.k.a., Arvo, fulfilled his vow to his former squad after his betrayal to blind a member of High Command," he said tiredly.

Despite being blinded, Ridley's hearing was still as sharp as ever. He turned in the direction of Arvo's voice. "And let it be known," Ridley responded with venomous hatred, "that on this day, Space Pirate Unit 1337, a.k.a., Arvo, was rightfully killed by the very squad leader he disgraced on the day of his betrayal. We won't be missing you," the space dragon snarled, and, with a swipe of his spiked tail, slit Arvo's throat.

Ridley grabbed the dying body and flew off, although he bumped into several walls along the way.

-=-=-

For the first time since her childhood, Samus was genuinely happy.

She enjoyed her profession as a bounty hunter, but it wasn't the same as being happy. Here, amongst Ashen Feather and White Voice, she felt at home. There was the looming danger of the Space Pirates and the X Parasites, of course, but she'd be damned if she'd let that ruin her time with the first Chozo she had seen since she was just a girl.

Mother Brain, however, had no reservations about reminding her of what needed to be done. She was talking with Ashen Feather when the floating avatar of Mother Brain approached.

"I have uncovered some new data I think you'd like to know," the machine said. "Federation troopers landed on the planet an hour ago. They recently did battle with Ridley and Kraid. Kraid was killed, and Ridley was blinded. Seven of them remain out of the sixteen that came."

"Why would Federation troopers be here?" Ashen Feather wondered.

Samus sighed. "It's my fault. I disobeyed their orders and destroyed some of their experiments, so now they've declared me a criminal. They probably sent the troopers after me to capture me or kill me."

"Quite likely," Mother Brain agreed. Samus glared at it with such intensity that even the machine recoiled a bit. It flew away, muttering something about having data to analyze.

"So, what were we talking about again?" Samus asked Ashen. The Chozo frowned.

"Samus, Mother Brain has a point. We should be focusing on how we can end all these threats."

Samus frowned back, and was about to respond when Ashen cut her off.

"I know it's been a long time since you've been among us, and I know that you want to spend time with us. That's fine, but there'll be plenty of time for such things after we've gotten rid of the threats." He smiled at her gently.

Samus was unable to come up with a sufficient counter-argument, so she merely grunted in reply.

"White Voice," Ashen Feather called, "would you kindly order Mother Brain to open the training chamber?"

"What for?" questioned Samus.

"To train you, of course," laughed Ashen Feather. "While the Metroid DNA may have terrifying effects, it has some useful ones, as well. We're going to try to draw the useful ones out more quickly. Come on!"


	5. Part 5

"This," Ashen Feather said, "is the training chamber."

Samus looked around in awe. The room was enormous, dwarfing even the long shafts present in Brinstar. A large bridge was in the center of the room, with bubbling lava below. "The training chamber is connected to all three major areas of Zebes," Ashen explained. "Maridia from above, Norfair from below, and Brinstar to the side. We've captured several native creatures to train you with…are you ready?"

Samus nodded her head. "Bring it on," she said.

"All right, then. Step onto the bridge. You have your Gravity Suit upgrade, right?"

Samus nodded again.

"Good. Then it won't make a difference when I do this." He pressed a button on the wall. Instantly, the door was sealed shut, though there was a window for Ashen to watch through. Moments later, a hatch on the ceiling opened, and water came flooding into the room, filling it almost completely.

Moments later, Samus heard a familiar roar.

The monstrous crustacean, Draygon swam downwards, letting loose another roar. The hatch closed after it, leaving Samus alone with the beast.

Draygon swooped down, attempting to grab Samus with its claws. The bounty hunter quickly rolled into her Morph Ball, narrowly escaping its grasp. She unrolled, then shot a few missiles at it. The explosives bounced harmlessly off of its thick hide.

Samus swore. When she had first fought a Draygon, she had used her Grapple Beam to conduct electricity from a short-circuiting machine in order to defeat it. This time, though, she didn't have her Grapple Beam…nor did she have access to such a device. She'd have to figure out another way to kill it.

There was no time for thinking now, though; Draygon was attacking again. This time, Samus was unprepared, and the crustacean's claws closed around her. She fired frantically, but it was to no avail. Draygon swam around, gaining momentum, then slammed Samus into a wall. Her armor cracked slightly with the force of the impact.

As she rose to her feet again, Samus fired a few more missiles. Most of them bounced off again, but one of them hit its exposed belly.

Draygon roared with pain.

A smile grew across Samus's face as she developed a plan.

Taking aim at Draygon's belly again, she fired off several missiles and a charged shot. Again, Draygon's pain was evident; in desperation, it attempted to grab her once more, but Samus was prepared this time. She rolled into Morph Ball form and lay a Power Bomb as she rolled off.

The crustaceous beast was smarter than it appeared, though; now knowing that Samus knew its weak point, it hovered above her now, not allowing her a clear shot at its belly. Occasionally, it would descend, swiping at Samus with its sharp claws, then quickly retreating to safety again.

Samus tried to get a good angle on it, but nothing seemed to work. Draygon was too fast for her to outrun, even with her Speed Booster.

Then, suddenly, she remembered why she was fighting – to hone her Metroid abilities…

Perhaps if she tried to tap into them…?

She took a deep breath, then concentrated on the part of her that was infected with Metroid DNA. As if in response, her claw-like hand seemed to pulsate.

Suddenly, the ground started getting farther away.

She had gained the ability to levitate.

Now, she was level with Draygon, allowing her to easily target its belly. She took aim, and blasted it to bits.

"Game over," she said smugly as the carcass sank to the ground.

Then, suddenly, she felt a brief pain in her arm. She quickly took off her armor to see what was the matter.

The Metroid DNA infection had spread to her elbow.

-=-=-

The color was drained from each and every one of the troopers' faces. In the aftermath of the battle, they were trying to decide what to do next.

"We have to get out of here," Wesley repeated for the fifth time. "It's too dangerous here. We need reinforcements. We need a LOT of reinforcements."

"By now, they'll have alerted the main pirate force," another trooper pointed out. "Even if we had the entire Federation army with us, we wouldn't stand a chance. They're completely prepared for us, and this is their home turf."

"We still have to get out of here."

-=-=-

Meanwhile, White Voice's face paled as he received the newest data. He hurriedly went to show Ashen Feather and Samus.

The X Parasites had discovered the underground caves.

-=-=-

"I'm not denying that we need to leave," the trooper responded. "But you need to calm down a bit. Stop hyperventilating and think- "

The sound of a large explosion from above interrupted him.

Everyone was silent. Several seconds later, the noise of heavy footsteps approached them.

"Everyone hide behind the giant lizard," hissed one trooper. They all gathered their weapons and did so. Wesley peered around the edge to see if he could discover what was approaching.

Moments later, he saw.

It was Samus Aran.

Without any thought but his own safety, he panicked. Abandoning his companions, he ran as fast as he possibly could, away from her. He knew that she would kill him for betraying her. He knew it.

He wanted to live.

Shouts and sounds of gunfire erupted behind him, but he didn't look back.

-=-=-

Ashen Feather stared at the screen grimly. "It's only a matter of time now," he said. "Tourian is difficult to reach, but it isn't impossible. The X Parasites will find us."

He turned to Samus. "When the X Parasites reach us, you must escape. You're the only one in the universe who can fight them. If they kill you…" He deliberately left the sentence without an ending.

"But what about you and White Voice?" Samus asked. Ashen Feather sighed. "We must remain here. We'll need to terminate the Mother Brain, first of all. If the X Parasites got their hands on it, they'd have access to our entire database. They'd know the location of every planet in the galaxy, exactly where every trace of civilization was. They'd spread through the galaxy more quickly than you could imagine. Plus, we need to destroy any ships we have here; if the X Parasites gained access to a space-faring vessel, it'd be just as catastrophic."

-=-=-

The pilot, after a long nap, awoke, suddenly. He quickly found out why; the communications radio was crackling. He quickly turned it on. "Pilot of GFS Odin to ground squad; do you read?"

The message came back quickly. "We read you, captain. We've successfully taken Samus prisoner. Please land ASAP."

"Right away."

He maneuvered the ship to where he had dropped them off, then landed. There were six of the troopers remaining. With them, Samus Aran stood with a large-scale explosive tied to her back.

The pilot frowned. Something seemed…off…about them. The troops and Aran herself all seemed…different.

He shrugged it off as nothing. He led them all aboard. As she passed him, though, Samus glanced at him briefly. He managed to catch a glimpse of the face inside the visor.

The eyes were completely blank.

Suddenly, blob-like creatures erupted from Aran and all the troopers, and everything went black.

* * *

Heavy footsteps echoed through the long corridor, accompanied by noises of hissing and spitting. Occasionally, the footsteps would stop, but they would soon resume their methodical march. Soulless eyes, masked by a green visor, flicked back and forth as the SA-X hunted its prey.

Tarus Wesley held his breath as the terrifying figure plodded through the tunnel. When he had bolted, he had been seen by the SA-X. After it had disposed of his comrades, it had begun its slow search for him. This on its own was frightening enough, but what absolutely terrified him was what he had witnessed it do later.

It _multiplied._

Wesley was, of course, still under the belief that he was being hunted by the real Samus Aran. A display of an oddity such as this would only serve to make him more fearful.

A buzzing noise filled the air. Wesley had long since identified all of the SA-X's techniques. The buzzing was an indicator that it had just launched itself through the air, surrounded by a swirling mass of destructive energy. He had nicknamed it the "Screw Attack", as it resembles a bolt being screwed in, somewhat.

The SA-X was approaching his rock, now. He was trying to gauge when he should swivel around it in order avoid being seen when a loud snarl filled the air.

"URMSHGA!"

Space Pirates.

-=-=-

"How far have the X spread now?" Ashen Feather questioned. White Voice conveyed the question to Mother Brain, who promptly replied, "They have reached the gate, but they are bewildered by the lock you have placed there. It is only a matter of time, however, before they call upon the X clone of the Hatchling in order to solve this dilemma."

Samus clenched her fist slightly.

"Samus," Ashen Feather said softly. "You'll have to leave now."

"No," Samus replied curtly. "Not yet."

"Samus, I know -"

"It's not about that," she responded, knowing what Ashen Feather was about to say. "It's a part of it, I suppose, but this is something else, mostly. I'll leave…but I want to do this, first."

Ashen Feather looked at White Voice for guidance. The mute Chozo nodded slightly. "All right," he conceded. "You know where the elevator is."

Samus smiled and hugged them both. "I'll see you again soon," she promised. She grabbed her helmet from where it lay on the floor and put it over her face. The familiar green visor greeted her, and it turned transparent after a moment. Her status appeared on the sides of the visor.

"Energy tanks…full. Missiles…full. All suit technology functional. Time to go kick some parasite ass," she muttered.

The rest of her armorsuit formed around her, and Samus left Tourian at full speed.

Mother Brain's eye gazed after her. "Suicidal girl," it commented before returning to its duties.

-=-=-

Wesley peered out from behind the rock at the confrontation that was occurring. A squad of Space Pirates, numbering two dozen, faced the emotionless SA-X, whom he still believed to be Samus. Their condition, though, oddly enough, seemed strange. Most of them had some form of injury. One of them had half its arm missing; another had a long slash along its abdomen and was bleeding a disgusting yellow fluid. What had happened to this group of pirates? Wesley wondered.

What appeared to be their leader – a pirate with its face brutally maimed – snarled again. The rest of the pirates snarled in response, and they all charged.

This was not a battle, Wesley quickly realized – this was a slaughter. The SA-X seemed unphased by the shots the pirates fired at it. It walked up to a pirate, still firing at the frightening figure, and knocked it over the head with its arm cannon. The next pirate's neck was snapped.

Despite the odds being against them, the pirates continued to fight even as they fell one by one.

Wesley noticed movement up above, on an overhang. He glanced up at it, and spotted broad wings, glowing yellow eyes, and a beak-like mouth.

Ridley. His eyes had been restored.

Their eyes connected for a moment, and they seemed to share a common understanding – that this battle was hopeless.

Then the space dragon flew away, and Wesley returned to watching the battle as if nothing had ever happened.

There was but one Space Pirate left, now. The SA-X approached it, seeming to take pleasure in causing this pirate's death.

And then a missile killed it before it could.

There, standing behind the collapsed pirate, was the real Samus Aran, standing in all her glory.

The SA-X wasn't impressed. It immediately fired off an Ice Beam shot at her.

Aran dodged and rolled into Morph Ball form. She lay a Power Bomb beside her foe as she rolled past it, but the SA-X countered by freezing the Morph Ball in its tracks before it could escape the blast radius.

Samus unrolled and fired a charged shot at the SA-X. The clone Screw Attacked its way through the shot, then fired one of its own. Samus Screw Attacked over it in turn. They both then leapt into the air as swirling balls of destructive energy, and crashed into each other. They both fell to the ground, harmed an equal amount. For now, it was a stalemate. The SA-X began its next volley of attacks.

Wesley was so busy watching this extraordinary battle that he failed to notice Ridley landing right beside him until it was too late.

He felt a claw close around his abdomen and a voice whisper into his ear, "You're quite the sneaky little rat, aren't you?" Cackling softly, Ridley flew off into the darkness with Wesley as his prisoner.

* * *

Samus leapt to one side, firing off a volley of missiles as she did so. The SA-X, in turn, rolled into Morph Ball mode and swiveled around behind Samus before she could discern what had happened. Several bombs were layed at Samus's feet, and the bounty hunter found herself knocked forward by the blasts.

Samus held her hands out in front of her and turned the fall into a frontward flip, however. She quickly turned around, and, spotting the ball out of the corner of her eye, fired a missile at the place where it would be in a moment. The sound of the SA-X in pain rewarded her.

Her nemesis returned to its normal form. Its blank white eyes, just barely visible behind the green visor, were narrowed into slits. It clearly hadn't expected Samus to be so skilled.

Samus made the next move, firing off a charged blast at the SA-X. It quickly dived out of the way, firing several shots at Samus. Much to her confusion, though, all of them missed. Surely the SA-X was a better shot than that…?

She got her answer in a moment as a giant form tackled her to the ground.

Samus found herself looking straight into the draconic face of her old enemy, Ridley.

"Surprise," Ridley snarled as he raked his claws across her armorsuit.

As the SA-X approached, the space dragon lashed his whiplike tail out at the Samus clone, sending it smashing into the wall. Samus used this opportunity to fire off a missile into Ridley's face, forcing him to let her go. The three combatants each separated, surveying the situation before engaging in an all-out three-way brawl.

Samus, gauging the SA-X to be a more immediate threat, instantly fired a missile at it. The clone had been concentrating on Ridley, so the attack caught it off-guard. The force of the missile caused it to go flying several feet before landing unceremoniously on its back. Immediately, Samus trained her sight on Ridley – or, at least, where Ridley had been an instant before. Where had he...?

Samus's unfinished question was answered in an instant as she and the SA-X were bombarded with fireball blasts from above. Ridley was flying above, using the high ceiling to his advantage. Samus sighed in frustration. She wasn't used to fighting a two-fronted battle with such powerful enemies.

In order to better combat Ridley's aerial capabilities, Samus tapped into her Metroid DNA and began levitating into the air.

A look of complete and utter disbelief crossed the space dragon's face as he witnessed this strange turn of events.

The SA-X's blank stare followed after the two of them, coldly calculating its options. Realizing that the aerial combatants would be hard-pressed to defend themselves from a ground attack while they were preoccupied with one another, it raised its arm cannon and waited for the proper time to strike.

Samus ducked under a swipe from Ridley's claws, and used the opportunity to smash his head with her arm cannon. The space dragon was dazed for a moment, and he lost some altitude. At that moment, the SA-X started firing.

Samus flew to one side just before a Super Missile collided with her. Ridley, however, was not so lucky; as it hit him, he was launched back…right into Samus. The force of the impact caused the bounty hunter to fall to the ground. The SA-X used the opportunity to fire off an Ice Beam blast at her, chilling Samus to the bone.

An enraged Ridley hit the SA-X with a flying tackle before it could do any further damage, though, allowing Samus to briefly catch her breath. She glanced at her energy and missile reserves, and started at how quickly her energy reserves had depleted. Of her original fourteen, Samus only had four energy tanks left. While she hadn't been hit by too many attacks, those attacks had been damn powerful…she had a decent amount of missiles remaining, at least.

The SA-X bludgeoned Ridley with its arm cannon, dazing the space dragon, then, with extraordinary strength, kicked him off of it. Climbing to its feet, the clone instantly fired three missiles at Samus. She managed to dodge the first two, but the third caught her off-guard, sending her crashing into a wall. She was then snatched up by Ridley, who flew up to the ceiling and held her against there.

"You and your little friends have been quite the nuisance," he growled. Little friends…? Samus thought, dazed. What was Ridley talking about?

"Either way, though, most of them are either dead or captured by me, and you'll be dead in a few moments, so your futile resistance will be over soon. Rot in hell, Aran!"

At that moment, Ridley began charging a large fireball to release at point-blank range.

Samus felt a distinct sense of déjà vu, and grinned smugly as she remembered a similar situation to this one that had occurred only a few days before.

"Space Pirates never learn," she murmured to herself as she latched onto Ridley's flesh with her arm. Claws extended from her fingertips and dug beneath the space dragon's skin as she began absorbing his energy.

This time, though, Ridley didn't back off. Despite the obvious weariness that was increasing as Samus absorbed more of his energy, Ridley continued charging the fireball. Only when he couldn't go on did he release the destructive burst of flame.

He then let go of Samus and fell to the earth, exhausted. The SA-X, knowing he could do little to resist, approached him.

As the fireball hit the bounty hunter, she felt as if she was being boiled alive. Her screams of pain reverberated throughout the caverns of Zebes, and she fell to the ground after Ridley.

Gasping with pain and exhaustion, Samus glanced at her energy reserves once more. No additional energy tanks left, and only 23 energy units. If she hadn't absorbed some of Ridley's energy beforehand, that fireball would have been enough to kill her.

The SA-X looked between its two helpless opponents, as if unable to decide which one to finish off first.

This moment of weakness was its downfall.

With the last of his strength, Ridley's fist collided with the SA-X, sending it flying back several meters…and landing right next to Samus.

Samus seized the opportunity immediately, plunging her Metroid-like claws into her clone and absorbing the X Parasite within.

The SA-X let loose an inhuman shriek, writhing and howling as its very essence was absorbed into Samus. The blank eyes disappeared beneath the visor as the very last of its life was sucked dry. Moments later, the armor disintegrated into dust.

Suddenly, Samus felt a movement behind her, and spun around just in time to block Ridley's tail whip.

Samus and Ridley stared at each other for a full minute, neither one moving. And then Samus noticed an emotion she had never seen before in Ridley's eyes.

Fear.

Ridley was still severely weakened, and Samus, after absorbing the SA-X, was at full power. Samus had the advantage here, and Ridley knew it. With a single shot, Samus could probably kill him.

Ridley was at her mercy.

Samus tried to press the trigger within her arm cannon to fire a missile, but her finger wouldn't seem to move. It was as if there was some unseen force preventing her from enacting her revenge on the being that had caused the death of her father and killed her mother before her very eyes.

Finally, Ridley leapt up and flew away, leaving Samus standing there with her arm cannon raised.

She swore to herself. She had just had the perfect opportunity to finally kill Ridley once and for all, and she had let it slip between her fingers. What was wrong with her?

Then, she noticed something strange. Even though Ridley was beyond her sight, she could still _feel_ his presence. It was as if she had been given a sort of sixth sense.

But she could feel something else around her, too – something much more distinct.

X Parasites.

-=-=-

Tarus Wesley had seen many odd things during his lifetime. But this? This beat them all.

There was nothing stranger than seeing a band of Space Pirates treat a Galactic Federation trooper with civilty.

Admittedly, this particular band wasn't in the best condition; like the ones he had seen earlier, this one was in poor condition. Each pirate had one or more terrible wounds – it was a wonder that some of them were still even alive, and he felt sick looking at some of them. But he'd take this civil, wounded band over the one he had just been rescued from any day.

They numbered no more than ten, yet they had been good enough to rescue him from the two dozen that Ridley had left him with without any casualties. Despite their wounds, they were good – Wesley would give them that.

One of the pirates served him a makeshift cup with some translucent yellowish-white fluid in it. Wesley sniffed it apprehensively, and realized with a note of surprise that it was a human beverage: lemonade.

"How did you get this?" he asked, bewildered. The pirate looked at him with annoyance, and Wesley realized his mistake. "…Right. Sorry. I forgot."

The pirates were drawing out their plans for something, that much was certain. They were huddled around one of the walls, holding some sort of black fluid that they seemed to be using as ink. Occasionally, one of the pirates would wipe the ink off and start anew.

When they finally withdrew from the wall to look at their handiwork, Wesley recognized one of the drawings there:

Samus.

Behind her were several Space Pirates, shooting at her. Were they planning a sneak attack?

But then his attention was drawn to what was in front of Samus: more Space Pirates – these ones bigger and stronger – led by Ridley. Wesley then realized that the pirates behind Samus weren't shooting at her, but at the other pirates.

They were planning an alliance with Samus Aran.

-=-=-

"President Rodriguez, sir. The ship sent after Samus Aran has returned with her in tow. What do you want to do with them?"

Rodriguez's eyes gleamed with triumph. "Send General Arvo and Tarus Wesley in with Aran."

There was a brief pause. "Sir, they've reported that both of them perished while trying to capture Aran."

Rodriguez considered this, then shook his head. It was a shame…Arvo was one of his best generals, and Wesley had potential. Oh well. He'd send a message to Wesley's family and memorialize their achievements.

"Right, then…just send in Aran with some of the ship's crew to escort her."

"Right away, sir."

Several minutes later, three people entered the office of one of the most influential men in the galaxy: Samus Aran and two crew members from the mission to capture her.

The moment they entered his room, Rodriguez could tell that something was wrong. He stood up to greet them, nevertheless, not betraying his suspicions.

"Well, I never thought I'd see the day when the great bounty hunter, Samus Aran, would be bound in chains," he said mockingly. Aran's head was downcast. Grinning on the outside, Rodriguez walked around his desk and stood directly in front of Aran. "Look at me while I'm talking to you," he hissed.

Slowly, Aran's head rose, and Rodriguez caught a glimpse of two blank, pure white orbs where Aran's eyes should have been. At that moment, yellow globs erupted from all three of them and rushed toward Rodriguez.

He recognized them immediately as X Parasites.

Rodriguez dove out of the way, trying to dodge the attack, but the parasite swerved suddenly and latched onto his body. Rodriguez watched with horror as the yellow glob disappeared into his skin.

The X Parasites had infected him.

Already, he could feel them multiplying within, absorbing his DNA. His vision blurred, and he began slipping into unconsciousness.

Then, his eyes latched onto a single object of hope lying on his desk, and he tried to walk over to it.

As soon as he stood, he was overcome by a wave of nausea, forcing him to sink back down to his knees. His head felt like it was spinning. Gulping, he went on his hands and knees and tried crawling to his desk. When he was halfway there, he erupted into a series of spasms and convulsions.

Attempting to get his body back under control, Rodriguez crawled the rest of the way to the desk, and collapsed at the foot of it. He tried to lift his arm, but it felt as if it was being weighed down by a two-ton object. He tried the other arm, and felt the same result. This was the end, he thought.

Then, he tried one last time. With strength he didn't know he had, he managed to lift one hand up onto the desk. It grasped around for the object of his desire, and felt the handle. He brought the hand down, and dropped the object beside himself. He didn't have much time left.

His hand shaking, he picked up the syringe and injected the green Metroid DNA into himself.


	6. Part 6

Rodriguez continued laying there for a minute or so, shaking uncontrollably. Slowly, he felt his sickness ebbing, his blurry vision returning to normal. Finally, he managed to stand up, leaning on his desk. There was no sign of Aran or either of the two crew members.

Suddenly, one of his attendants came bursting in. "Sir! I heard a crash! Are you - ?"

Rodriguez grabbed ahold of the man's shirt. "Order a bioscan for X Parasites. Now." His voice was even, but just barely.

"Sir…?"

"I SAID NOW!" Rodriguez screamed, throwing the man back. Startled, the attendant retreated to do as he was told.

Rodriguez bent down and picked up the now-empty syringe, nervously glancing at the spot on his arm where he had injected it. He had kept the Metroid DNA on his desk for safe-keeping, to ensure that nobody ever found out about it. He had been planning to dispose of it once the Metroid breeding project was well underway, but he wouldn't have to worry about that now…

His thoughts turned to the crew members. All of them were probably infected. They could be spreading X Parasites like the plague now that they had access to the Federation capital…

He glanced toward the comm device. With luck, the epidemic hadn't spread to the security team yet…

"Security," he called into the device.

"What is it, sir?" a voice responded. Rodriguez prayed with all his might that this would work.

"I want the Galactic Federation capital to be placed under total lockdown. NOBODY is to enter or exit until I say otherwise. I repeat, NOBODY. Lock down all the entrances and exits. "Any and all openings must be COMPLETELY sealed off. This is an emergency. Do I make myself clear?"

"Affirmative, sir," the guard responded.

Rodriguez sighed in relief as he received word that his orders had been carried out. Now, there was the issue of rounding up everybody who WAS infected…

The attendant then returned, his face pale.

"Sir…I ran the scan. One eighth of the complex has been infected with X Parasites, and they're spreading. Fast."

He looked positively terrified.

"Which sector are most of them in?" Rodriguez demanded.

"Sector 7, sir," the attendant responded. Rodriguez was already on his way to the comm device.

"Security! I want all routes to Sector 7 completely and totally sealed off ASAP! The lives of everybody in the capital complex are at stake here!"

"Right away."

The attendant frowned. "Sir, not all of them are in Sector 7. There are a number of them all over the facility. They can just multiply and spread until they've taken over the entire capital."

"That's where I come in," Rodriguez muttered.

"What?"

Rodriguez looked over at the attendant. "Give me a list of every single infected person in the facility as of right now, then broadcast an announcement to keep clear of them. I'll handle them myself."

The attendant gaped at the president. "You can't be serious! They'll infect you just like everybody else!"

"I know what I'm doing," Rodriguez snapped. "Now go before they infect more people."

Hesitating for a moment, the attendant ran back to the room to compile the list.

Rodriguez headed over to a storage room, located in the back of his office. He kept a variety of personal belongings that couldn't fit in his desk in there.

He gazed at the Federation armorsuit that he had used during his time in the military. It had been nearly twenty years…he hoped he still could fight efficiently.

He strapped himself into the armorsuit. Glancing around, he set his sights on an insect on the other side of the office. He aimed, and fired.

The insect was hit dead-on.

Rodriguez grinned. "I've still got it," he chuckled.

The attendant came racing back with a piece of paper in his hand. "There are about fifty people on there," he said, panting for breath. "I've also broadcast a warning that all of them are infected, just like you asked me to," he added.

Rodriguez nodded, his eyes scanning down the list. All of them were important generals and politicians. The X had chosen their targets well. Under different circumstances, they could have easily organized a coup and overthrown the government from within.

Rodriguez perused his mind, trying to see if there was anything he had forgotten. He couldn't think of anything.

"I'll be back," he promised the attendant before jogging off to confront the X Parasites.

On his way there, he thought about what he would do with the ones trapped in Sector 7. He could just wipe them all out, but…this was the perfect opportunity to study them up close that he had been waiting for. Perhaps it was best to keep them alive…yes, that's what he would do.

The ones who were roaming the capital, though, would have to die.

-=-=-

Samus wearily returned to Tourian, White Voice and Ashen Feather greeting her.

"Excellent work out there, Samus," Ashen Feather said. White Voice nodded his agreement.

"I let Ridley get away, though," Samus muttered angrily. "I could've finished him off for good this time."

Ashen Feather shook his head. "We both know that's not true, Samus. The Space Pirates probably would have just cloned him like they always do."

The bounty hunter sighed and nodded. "I guess you're right."

Mother Brain's eye approached. "You may have triumphed, but just barely. Without Lord Ridley's attack on the SA-X, you would have been defeated."

White Voice's eyes widened at Mother Brain's usage of the phrase "Lord Ridley", but neither Samus nor Ashen Feather seemed to notice Mother Brain's slip-up.

"In the future, you should be more careful, whether you're fighting an SA-X, Ridley, or both."

It was not lost on White Voice that Mother Brain had corrected its mistake, this time omitting the "lord".

Samus glared at the computer. "You underestimate my ability. I could easily take either one of them one-on-one."

"Arrogance will be your downfall," Mother Brain responded. "One sneak attack, and it could be all over for you."

Samus grinned. "Sneak attacks won't be a problem anymore."

"What do you mean?" asked Ashen Feather, confused.

"I'm not sure if this is another extension of my Metroid abilities or the result of absorbing the SA-X, but I can sense the presence of life-forms for quite some distance around…I'd estimate approximately half a mile. In addition to that, I can specifically identify X Parasites."

Ashen Feather blinked. "That's…that's quite the power you have there, Samus."

She nodded. "It'll definitely come in handy, that's for sure."

"Well, regardless of special powers, it's still foolish to be reckless. You need to be careful, Samus," said Mother Brain.

"I'll be…"

Samus stopped in mid-sentence. Her face paled.

"X Parasites. They're coming down here."

"Mother Brain, engage all security measures!"

There was a pause. "The security system seems to be jammed, for some reason." White Voice narrowed his eyes at this.

"Not good," Samus whispered. "I'll have to fight them off."

Ashen Feather frowned. "How many are there?"

"Several hundred. More and more are coming…"

The Chozo closed his eyes. "Samus. You remember what we told you before you went off to fight the SA-X, don't you?"

Samus nodded, a lump forming in her throat. "That I need to escape while you and White Voice terminate Mother Brain. Right."

Ashen Feather put his hand on Samus's shoulder. "Good luck, Samus. I am honored to have met you."

He knew he was going to die.

Samus's mind was filled with protests as she walked away, toward the secret exit from Tourian. _This isn't right!_ she screamed mentally. She couldn't leave White Voice and Ashen Feather to die like this when they had shown her so much kindness, no matter what they told her to do! But how could she stop this from happening?

* * *

While Samus headed toward the exit from Tourian, Ashen Feather and White Voice turned to Mother Brain's chamber. White Voice appeared to be in deep thought about something – then again, he always was, Ashen Feather noted with a small smile. He wished his friend could talk, so that White Voice could actually share what he was thinking. But then again, he supposed, there was no point in wishing for what could never happen.

They stepped over the threshold into Mother Brain's chamber…and the door locked behind them.

Ashen Feather frowned. That wasn't supposed to happen…

The bridges leading to the Mother Brain were retracted, as well. What in the world was going on here?

As if it had heard Ashen Feather's unspoken question, Mother Brain's avatar hovered over to them. "You've finally arrived," it said.

"Mother Brain! Please extend the bridges so that we can deactivate you. We haven't much time."

"I'm afraid that I can't allow you to do that," the mechanoid responded to Ashen Feather. "If you deactivate me, then I won't be able to kill you."

Ashen Feather's breath caught in his throat, though White Voice didn't seem to be quite as surprised.

"What?"

"I purposely referred to the Space Pirate leader as 'Lord Ridley' earlier. This was intended to lure you two and Samus Aran to my chamber to investigate, so I could dispose of all three of you. Unfortunately, you and Aran were both too engrossed in your discussion to notice this, though White Voice easily caught it."

Mother Brain's eye turned to White Voice, who glared at it in response.

"So, as an alternative, I disabled all of the security systems to allow a horde of X Parasites in. This would force the three of you to come and deactivate me to ensure that the X wouldn't get their hands on the vital information I hold. It would appear that my plan has worked."

"Not quite," responded Ashen Feather. "You don't have Samus. She's on her way out of here as we speak."

"Is she?"

Ashen Feather opened his mouth to say yes, but he hesitated. Samus _was_ rather headstrong…could she be trying to rescue himself and White Voice before escaping?

"It doesn't matter," he decided. "Samus has destroyed you twice before. She can do it again!"

"Both of those times, she had her armorsuit," Mother Brain responded. "I intend to remove that factor from the equation. Tell me, have you checked your equipment since you entered this chamber?"

Ashen Feather frowned, not quite seeing what Mother Brain was getting at. He glanced down at his stun pistol. It wasn't anything special, a simple Chozo-made weapon for self-defense. Nevertheless, it came in handy in tight situations. He tried firing it at Mother Brain's avatar.

No shots came out.

He tried several more times before giving up and looking at his other equipment. None of it was working.

"A field has been installed in this chamber," Mother Brain explained, "a field that renders all Chozo technology useless. When Samus Aran finally enters, she will be powerless."

"Then how are you working…?" asked Ashen Feather.

Mother Brain's eye gleamed. "Because I am no longer Chozo technology, but Space Pirate technology."

And then Samus burst through the door.

-=-=-

Rodriguez scanned the area, making sure that there were no more infected people in the area. "Do another scan for X Parasites outside of Sector 7. Give me the results as soon as they come in," he ordered over his comm device.

"Right away, sir," was the reply.

A minute later, he got his results. "It's strange…all the X Parasites have disappeared somehow. Maybe they've somehow gotten cloaking technology."

Rodriguez smiled in satisfaction. "No, I don't think that's the case. I think we don't have to worry about them any longer."

"What makes you say that, sir?"

Rodriguez glanced down at his arm, to the spot where he had injected the Metroid vaccine. "Just a feeling."

He began taking off the armorsuit. "Anyway," he said, "we now have a good amount of X Parasites to do research on. Sector 7 should remain sealed off for now, but we can reopen the rest of the capital. I want all the best scientists working on a way to prevent infection from the X so that we can further study and experiment on them. Got it?"

"Of course, sir."

Rodriguez's smile grew. Soon, he would usher in a new era in the Galactic Federation. Soon, the X Parasites would become the downfall of the Space Pirates, Samus Aran, and anybody else who threatened the Federation's rule.

He couldn't wait for that day to come.

* * *

"Admission granted. Opening Sector 2 gates."

President Rodriguez waited impatiently as the agonizingly slow doorway opened. The doorway was more than a bit old, and it showed. They'd have to replace it in the near future.

The head of the project greeted him as he stepped into the sector. "President! What brings you here on this fine day?"

_What a suckup,_ thought Rodriguez. His predecessor had appointed him to the job because he was always so supportive of the president. Rodriguez had intended to fire him when he took office, but when he saw how skilled he was at his line of work, he decided, however grudgingly, to let him keep the job. That didn't make his constant attempts to get in Rodriguez's favor any less annoying, though.

"Business as usual, Weran," Rodriguez responded. "We've gotten a couple of new samples that I think you'll be interested in."

Weran's eyes gleamed. "Oh, really? Do tell!"

Rodriguez took out several vials filled with DNA. "I've gotten DNA samples from the Arbezt, the Yizafet, and even the Zaratans and Zapaltans…but I think this last one is what will interest you the most."

He put the others down on the table as he handed the fifth vial to Weran.

"Chozo DNA."

Weran's eyes widened. "How in the world did you manage to get this?" he asked in awe.

"Aran," replied Rodriguez simply, and Weran understood.

"I see…well, I thank you from the deepest depths of my heart for these vital additions to my research, President! I hope to see you again soon!"

"There's one more thing," Rodriguez said suddenly. "In the near future, I should be able to provide you with X Parasite DNA."

Weran's jaw dropped, and Rodriguez decided to leave before the man could question him further. He descended further into the sector to see how the research was coming along.

The G.F.S. Valhalla served as an outpost for the project, mostly where the DNA transfusions were conducted. But Sector 2 of the Galactic Federation capital served as the project's main base.

Few DNA transfusions actually occurred there, for fear of escaped specimens; on the Valhalla, at least, they'd be limited to the ship and there was little to no chance of somebody unintended seeing them. But on the Federation capital, where so many people came and went on a daily basis, it was much riskier. Rather, it served as a research center. The research conducted in Sector 2 would be sent to the Valhalla, where it would be used for experimentation.

One of the more recent breakthroughs was the discovery that it was possible for DNA transfusion of three or more specimens. The resulting creature was significantly more unstable, but they were hard at work on finding a way to fix that.

Satisfied with the state of things, Rodriguez left for his next destination: Sector 16, where research on Metroids was being done.

-=-=-

"What the -" Samus explained as her visor and HUD went dim.

"What's going on?" she demanded.

Mother Brain's eye focused on her. "As I was just telling these two, this was a trap for you," it said. "You've fallen right into it."

"You should've just left like I told you to, Samus," Ashen Feather said, shaking his head. "Then, at least, our deaths would not have been in vain."

"You are too headstrong, Samus," Mother Brain said. "That is your fatal flaw. You do not know when it is best to retreat rather than stand and fight. It almost got you killed earlier, and now it will kill you here."

The turrets aimed at Samus, Ashen Feather, and White Voice.

Then, suddenly, an explosion came from above.

"Space Pirates!" gasped Ashen Feather as they came jumping down the hole that their bomb had just made in the ceiling. The turrets aimed at them, now.

"Ah, the traitors," Mother Brain murmured. "Come to rescue your supposed savior, I see."

"URMSHGA!" they roared as one, and Mother Brain's eye zipped back to the actual being.

"How…intriguing."

Samus was confused, but, oddly enough, Ashen Feather and White Voice seemed to understand what they were saying just fine.

"Up here!" someone hissed from above. Samus looked up, and started in surprise. There was a Federation trooper leaning over the hole in the ceiling. Not just any Federation trooper, either; it was the one from earlier.

The one who had betrayed Samus.

As if sensing her remembrance of the event, the trooper flinched slightly, but continued beckoning upward. "The pirates will distract Mother Brain! You three need to get out of here!"

Still hesitant to trust Wesley, but seeing that she had no other choice, Samus obediently climbed up, helping Ashen Feather and White Voice as she did. Her visor returned to normal as she exited Mother Brain's anti-Chozo technology field.

Her arm cannon immediately went up to Wesley's forehead.

"What's going on here?" Samus demanded, her voice low. "Why are you with these Space Pirates? Did they threaten your life if you didn't join them?" That last sentence was said in a mocking tone.

"They're on your side!" Wesley hissed. "I don't know all the details, but they want to revolt against the rest of the pirates!"

Samus' eyes widened, remembering a certain pirate trooper who had helped her earlier. There were more of his kind…?

"We can find out the details, then," Ashen Feather said. "We've got translators back in the main section of Tourian. If we can manage to get there…"

"That won't be a problem," Wesley said, pulling out another bomb. "I'm in charge of our escape route, so I've got plenty of these. Just tell me where to drop it."

They began to crawl through the makeshift tunnel, and Samus grudgingly followed, still not trusting him.

Ashen Feather had Wesley drop the bomb in the area just above the storage room. A quick explosion later, and a hole was opened in the ceiling. Ashen Feather dropped down, and when he came back up, he had several chips in hand.

"Standard Chozo fare," he explained, handing out chips to Samus and Wesley. "Just put it in your ear, and over 2000 languages can be translated into one of your choice."

The two did so, both assigning the language of choice to Basic, the standard language throughout the cosmos.

"Now, we just need to regroup with the pirates, and we can be out of here," Wesley said, grinning at his companions. Samus didn't grin back.

They crawled back to the original hole above Tourian, and found the pirates waiting there, beating Mother Brain's mechanical eye senseless with metal poles.

Samus resisted the urge to smile and join in, instead choosing to stand aloof from the rest.

"Everyone," Wesley said, "this is Samus Aran and her friends…er…"

"Ashen Feather and White Voice," Ashen Feather finished for him.

"Right. Anyway, thanks to their technology, we can understand you now…"

One of the pirates stepped forward. "It is an honor to meet you, Samus," he said.

"Don't call me Samus," the bounty hunter replied curtly. "I only allow my friends to call me that, and I'm still not sure if I trust you."

The pirate was taken aback. "Yes, well…my apologies. I am Unit 9001, also known as Odius. I won't object to you calling me Odius, either."

"Odius," Ashen Feather said. "You're a Space Pirate. Do you have any idea how Mother Brain became affiliated with your people again?"

Samus was surprised. Nobody had told her that information…

"There's a tunnel behind the Mother Brain," Odius replied. "It's well-hidden, and few know of it. The pirates approached the Mother Brain from this tunnel and retooled her to their liking. I'm not sure if the mind of the High Command member was uploaded to her, but it's unlikely – I don't think they have access to it from here."

Odius turned to Samus again.

"Anyway, Sa – Miss Aran…I'll keep this brief. We are a group of renegade Space Pirates who have become dissatisfied with our lives as members of the Space Pirate Empire. We have come here to ask for your assistance in bringing the empire down. Will you help us?"

* * *

Samus frowned. To consort with Space Pirates, to cooperate with her sworn enemies…it went against everything she had ever known. And who was to say that these pirates were sincere? They could be plotting against her, intending to bring about her demise…

"I…" She hesitated.

The bounty hunter looked around at their small gathering. Odius and the other Space Pirates…White Voice and Ashen Feather…and Tarus Wesley.

_The Space Pirates, the Galactic Federation, and the X Parasites,_ Samus thought. That was what she was up against. Could one woman – even a woman of her strength – hope to stand up against all three of those threats?

_It can't be helped._

"I'll help you."

There was a bitter taste in her mouth after saying those words.

Odius nodded approvingly. "Thank you. With your help and the Galactic Federation, perhaps we can find a way to bring down the Space Pirate Empire."

Samus frowned. "You won't find any help from the Federation," she pointed out. "They're just as bad as you – your people, I mean. They just hide it beneath a façade of benevolence."

"That can't be," Odius said, a confused expression crossing his face. "They've done nothing but good for the galaxy since their establishment."

Samus shook her head. "The current president is steering it away from that direction. They've been doing inhumane experiments, treating people like lab animals…they've even gotten some of your DNA to infuse with their test subjects."

"And yours," Wesley interjected suddenly.

Samus turned to the man who had betrayed her slowly.

"What do you mean by that?" Samus asked, glowering at him. Wesley wilted at her stare.

"The president told me," Wesley explained weakly. "During on operation on you, they extracted a sample of Chozo DNA from your body…they're intending to use it on Project Werehuman."

"You need to learn to explain these things," Samus snapped. "What's this project? Is it what we saw on the Valhalla?"

Wesley nodded. "It's essentially a project to create the perfect supersoldiers, using the deadliest assets available to them. That's about all I've been told…"

He scurried back to hide behind the pirates, afraid that Samus might lose her restraint.

"Perfect," she muttered, walking over to a wall and kicking at it. "This is just damn perfect."

The very thought of those sights she had seen aboard the Valhalla was enough to make her sick. But now, knowing that the Federation had a sample of what made her the valuable weapon that she was…they could place the entire galaxy under martial law if they managed to use it successfully.

Odius looked around. "I don't see what the problem is," he commented.

Samus whirled around, rage evident even through her visor. "The problem," she spat, "is that the Galactic Federation can make a thousand Samus Arans and put the entire galaxy under their control. With my DNA, they can do everything that they couldn't before!"

Odius seemed unfazed. "So what?" he asked. Samus was about to respond when he interrupted. "They may have your strength. They may have your abilities. They may even have your armorsuit, if they can reverse-engineer it. But there's one thing they won't have."

Odius pointed at Samus.

"Your experience."

"What…" Samus began, but Odius interrupted again and pulled out a handheld computer system.

"2073 C.C.," he read aloud. "The Hunter clad in metal has decimated our forces on Zebes and destroyed two members of High Command - Mother Brain and Ridley. Research reveals the Hunter not to be a male cyborg, as our sources recently suggested, but a female human, named Samus Aran. It is highly recommended that she is disposed of before she causes further troubles.

"2075 C.C.," he continued. "The Hunter has once again disrupted our operations. All research regarding Phazon has been lost, along with the Phazon itself. The rebuilt Ridley has once again been incapacitated, as well. She is quickly becoming more than just a thorn in our side; if we are to achieve galactic domination, we must either kill or subvert her.

"2076 C.C. Three times, now, the Hunter has defeated us. In our debilitated condition, we were barely even a match for her. It has become clear that she will not be easily murdered; we must resort to our second option: to subvert her.

"2077 C.C. Even the subversion of the Hunter failed! The means were available to us, yet still we could do nothing to her! Some are beginning to wonder if she is some undefeatable goddess, incarnated into mortal flesh. No matter what she is, the damages done to us go beyond anything she has caused before. All of our Metroids are killed, all the Phazon in the universe has been eradicated, and Ridley, reanimated once more, has been once more disposed of. We wonder if the Space Pirate Empire will ever recover.

"2080 C.C. After three long years of rebuilding, the Hunter has undone all of our efforts in one fell swoop. Ridley and Mother Brain killed again, the Metroids extinct, and Zebes not only damaged, but destroyed outright. Well over half of our troops were stationed there; it is doubtful that we will ever fully recover from this loss."

Odius put away the computer.

"Don't you see? Your strength isn't what has let you do what you've done. Rather, it _is_ what you've done. If the things that are happening right now had occurred before your first mission, you'd be dead already. So what makes these supersoldiers that the Federation is making any different?"

Samus blinked. "You seem to feel pretty strongly about this," she observed. Odius grinned grimly. "I've suffered years of mistreatment from the Pirate Empire," he explained. "I won't have my one hope of breaking free doubting herself."

"Well, then," Samus said, straightening. "You've certainly invigorated me, but we still have a problem: what do we do next?"

Ashen Feather cleared his throat, suddenly. "If I may," he said, "I have an idea."

-=-=-

An unfathomable distance away, three old Space Pirates glanced toward the holoscreen as it lit up, showing the visage of Mother Brain. They put their frail hands on the receiver as the message began.

_"We are X,"_ Mother Brain said as yellow splotches appeared all over its form. _"We have a proposal for you…"_


	7. Part 7

"First of all," said Ashen Feather, "what is the current condition of the Space Pirates? The bad ones, I mean," he added quickly.

Odius contemplated this for a moment. "Not very good. Since the SA-X was freed, nothing seems to have been working to their benefit. Their troops have already been split into three factions: ourselves, the pirates remaining loyal to High Command, and the pirates that succumbed to the X. Only the last one seems to be in any good condition."

Ashen Feather nodded thoughtfully. "Then the Galactic Federation should be our main concern. They're the most direct threat to us at the moment…well, aside from the X, of course, but killing them all off isn't very feasible at the moment. We should probably -"

"The Metroids," Samus gasped suddenly. Ashen Feather blinked. "What?"

"I had almost forgotten…the Federation still probably has a Metroid breeding facility somewhere out there. If we could get a hold of a sizeable amount of Metroids, then we could set them loose on the X and end that threat just like that!"

Ashen Feather frowned. "That's great and all, Samus, but we don't know where -"

"Lycas," Samus replied promptly. "I was planning to head to that planet before I got entangled in this mess. It's a cold planet on the fringes of Federation space; ideal for storing Metroids while maintaining a low profile. Plus, there's a Federation vessel stationed there, so the planet must have something of importance."

Odius glanced at Samus skeptically. "Are you sure about this? It sounds to me like you're basing this plan on instinct alone."

Samus smirked. "It was instinct that got me through all those experiences you mentioned, as well," she retorted.

-=-=-

"Mr. President, sir?"

Rodriguez glanced up, his hand quickly disappearing from view. A nervous-looking man was at his door – a scientist, based on his uniform.

"Come in," he greeted the man. "What can I do for you?"

The man shuffled in tentatively. "Well, sir, I'm one of the workers assigned to the X project…"

At this, Rodriguez listened in closely. "And? Have you made progress?"

He nodded. "We have, sir. We've discovered an X-repellant that can be used on Federation uniforms to prevent infection from the parasite. We may now begin more intensive study of the organisms…is there any particular subject area you want us to research?"

Rodriguez assessed his threats for a moment. Aran, of course, came to the forefront of his mind…the X had been a fake, of course, so the real one was probably still out there somewhere…

"Two things," he said. "First, I want you to find a way for us to take control of the X, so that they won't turn on us. Second…I want you to find a way to remove their weakness to Metroids. Got that?"

The scientist nodded. "Of course, sir." He backed out of the office and left.

Now that he was alone once again, Rodriguez went back to studying his hand.

His translucent, sickly green, clawed hand…

-=-=-

"Careful, now," Odius whispered. "The X hadn't found this place when I last checked, but things could have changed. Samus, you take point."

The bounty huntress nodded and moved ahead of the others. Even she had never discovered this exit to Crateria in her prior visits to Zebes…it only reinforced what she had known all along: that almost every world she visited was an enormous, confusing maze that she could never hope to fully explore.

She walked out into the light, swiveling her arm cannon back and forth in search of threats. There was no sign of any, but you never knew.

"Our ship should be just beyond those trees," Odius murmured.

Samus nodded and started forward, eyes ever-watchful.

_Clank._

Her ears pricked up as she heard the distinct sound of metal. Someone else was there…

_Clank._

There it was again.

She signaled for everyone to stop, and her eyes scanned the surrounding area. She couldn't see any sign of –

_There!_

A brief flash of yellow, orange, and red in the trees, and Samus knew what she was up against: another SA-X.

Did it know that they were there, though?

Samus remained frozen in place for a minute, giving the SA-X enough time to get away from them. At last, she started forward again.

As she walked through the trees, though, she began to sense that something was odd. No sounds followed her…shouldn't the others at least have been making some sort of noise?

Finally, she had the sense to turn around. The others weren't there.

"You've got to be kidding me," Samus groaned as she turned back in search of them.

-=-=-

Wesley, White Voice, Ashen Feather, Odius, and the rest of the Space Pirate renegades waited with bated breaths as Samus walked forward. They were to follow once Samus had reached the trees…

Suddenly, she stopped. The others glanced at one another, as if to ask why.

Then, she simply disappeared.

Their eyes widened in surprise, and they took this as a sign that they weren't safe. They turned to leave…but there was Samus again, right there behind them.

"What -" Ashen Feather began, but Samus placed a finger to her lips and beckoned for them to follow her. She turned and walked back into the caves, and the rest followed.

Wesley frowned, though. Something seemed off about this…

* * *

"Have you heard?"

"About the president?"

"He's gotten so weird since the incident earlier…"

"And why is he wearing that glove now?"

Whispers and furtive glances followed Galactic Federation President Martin Rodriguez as he walked through the corridors of the Federation capital. They couldn't be helped; what with all the strange occurrences lately, rumors were bound to fly around. He could try to dispel some of them, but they would only be replaced by new ones. Better just not to address them.

He flexed his hand again, marveling at the way the claw bent and stretched in ways the human hand could never do. He was fascinated by this transformation, and, more importantly, eager to learn what sorts of powers it gave him. That would have to wait, though.

Because right now, he had three very important visitors arriving. He glared down the hallway as he thought about them, hatred boiling up inside of him.

Oh, yes. Three very important visitors indeed…

-=-=-

"Samus…I don't think heading this way is a good idea," Ashen Feather pointed out as they headed deeper into the caves. "We're going to run into a group of X, and if that happens, you'd be hard-pressed to defend all of us."

The bounty huntress didn't respond.

"We should probably go back," Odius agreed. "Whatever you led us away from out there can't be _that_ bad, and we at least have a chance of escape."

Wesley nodded faintly, the wheels in his head turning as he struggled to figure out what was wrong. Samus wasn't talking, of course, that was one thing, but there was something else…

_Clank, clank, clank…_

The distant noise of footsteps interrupted his train of thought. Metal footsteps…then they were one of the Samus clones!

"SA-X!" Odius gasped. "One of them's found us!"

"We'll back you up, Samus," Ashen Feather said. "You've held your own against one before; you can do it again, I'm sure."

Samus nodded silently, and Wesley began to piece everything together.

-=-=-

Voices echoed down the corridors of Zebes. They couldn't be too far now.

Samus checked her condition. Everything seemed to be in decent shape…she could probably save her allies without too much trouble. With any luck, they would help her out, as well…

As she rounded the corner, all of them came into sight. "There -" she began before being forced to duck out of the way of about eight shots.

What were they doing?!

She instantly fired off a charged shot at the SA-X before the rest of her allies – enemies – whatever resumed fire on her again. Samus rolled up into morph ball mode and rolled between their legs, dropping a few bombs in the process. The bombs wouldn't injure them; just knock them off-balance, that was all…

The SA-X had been content to hang back until there was a direct threat to it, but now it moved at a surprising speed, striking Samus with an Ice Beam. The bounty huntress unrolled and fired off an Ice Missile in response. Several more shots whizzed by her from her allies at the same time…well above her shoulders. Did they really have such terrible aim?

"Samus!" Wesley gasped suddenly, seeing the Ice Missile. Samus rolled her eyes. Great. _Now_ he could see the obvious?

Samus continued her assault on the SA-X as the rest of them, sans Wesley, aimed at her. "Stop, stop, stop!" Wesley shouted, getting in front of their weapons. "We've been tricked! It's Samus!"

"What are you talking about, you idiot?" Odius asked. "That's the SA-X. Can't you tell by its oversized shoulders?"

_What the…I don't have oversized shoulders anymore,_ Samus thought in surprise. She leapt to the side, avoiding a missile from the SA-X.

"We're being tricked!" Wesley repeated. "The SA-X doesn't have -"

"Out of the way," Odius snapped, pushing Wesley off to one side. "You're going to get us killed at this rate."

Wesley turned to Ashen Feather and White Voice. "Won't you listen?" he asked.

"Make it quick," Ashen Feather said grimly. "We don't want to stand around for long."

Meanwhile, Odius and his half-dozen troops came to the SA-X's aid, firing off their energy pistols at Samus. The clone nodded in satisfaction.

Samus did her best to dodge them, but a few still singed her armorsuit. She gritted her teeth in annoyance. This was not going to be enjoyable…

"It used the Ice Missile," Wesley pointed out.

"And your point is…?" Ashen Feather asked.

"Only Samus has the Ice Missile," argued the former Federation trooper. "It has to be her!"

"The SA-X easily could've copied it," replied Ashen Feather.

"But the one we think is Samus is still using the normal missile! She wouldn't stop using the Ice Missile for no reason!"

Ashen Feather sighed. "Fine. But that doesn't explain why what you're claiming to be the SA-X has Samus' Fusion Suit and why Samus has the original Varia Suit."

Wesley had no answer to that.

Samus went back into morph ball mode, having no choice but to unload her most powerful attacks. She planted a Power Bomb in the SA-X's vicinity and sped away, praying that Odius and his troops would have the sense to get out of the way of the blast.

They did, but they were also still unaware that she was the real Samus…so as she rolled through them, one of them managed to stop her and fired upon her.

Samus unrolled and stumbled back, frantically trying to escape from the stinging energy bullets. Behind her, the Power Bomb went off, and suddenly, Odius pushed her back into the blast radius of the miniature nuclear weapon.

Her eyes widened, and she let out a bloodcurdling scream as her entire body was wracked with pain. She maintained just enough focus, however, to fire off her grapple beam at the SA-X and drag it into the blast, as well…

The illusion faded as both Samus and the SA-X fell to the ground, seemingly trading positions. Their armor was cracked and shattered in some places A viscous yellow fluid bubbled up from the SA-X's form.

"Wha…" Odius began. "What just happened?"

Ashen Feather's eyes widened in realization. "That SA-X must've plundered our technology," he murmured. "We had an advanced light-bending device…it can be used to camouflage the user and can be linked to a related Chozo-made device – such as Samus' armorsuit. The SA-X made us think that it was Samus and Samus was it…"

"We have to get out of here," Wesley said, his face pale.

"I'll lead us to the ship," Odius said. "The Chozo can carry Samus. Wesley, you keep guard."

-=-=-

Their walk to Odius' ship was uneventful. When they got to the (relatively cramped) spacecraft, they set Samus down on the sole bed. She hadn't moved at all.

"Is she going to…" Wesley began, but he couldn't finish the sentence.

"I don't know," replied Ashen Feather, removing the helmet. Her face was chalk-white, except for the rivulets of crimson blood streaking down her face from the cuts. The Chozo stroked her yellow hair sadly. "I don't know."

Odius seemed the most depressed of all of them. He had been the one to cause this, after all…

As they lifted off and the world of Zebes shrank below them, things could not seem any bleaker.

* * *

"Her pulse is getting slower," Ashen Feather said with concern.

He hadn't left Samus' side since they had taken off. Wesley was curled up in the back, trying to catch some sleep. Odius was piloting the ship, his yellow eyes not betraying the guilt he felt at having caused this disaster. White Voice sat in a corner, contemplating something or other. They had dropped off Odius' troops at an outpost earlier; a squad of Space Pirates would be difficult to maintain alongside everyone else.

Odius' eyes flickered from the navigation screen to Samus and back. "We're almost to the hospital," he said. "Drulus should be able to take care of her."

"Are you sure?" Ashen Feather asked. White Voice glanced up keenly. "Because this Drulus fellow, competent as I'm sure he may be, doesn't have access to all the assets that the Federation does."

Odius sighed. "We've already gone over this," he said. "If we take her to a Federation hospital, all of us will be arrested. Besides, I'm sure that Drulus' aid will be enough."

Ashen Feather shook his head. "No. It won't be."

Odius quirked an eyebrow. "It's just a Power Bomb injury. Drulus has treated injuries on par with that in the past."

Ashen Feather shook his head again. "It's more than that." He gently pulled open Samus' mouth and pointed to her teeth. They had become sharp and elongated, almost like a vampire's. "The Metroid DNA is running rampant through Samus' body. Before, it would seem, her willpower was enough to keep it at bay. Now, though, there's nothing to stop it."

Odius stared incredulously at Ashen Feather. "And you expect that the Federation doctors will be able to stop it?"

"At this stage? No. I do not expect anyone to be able to stop it. But if the Metroid DNA runs unchecked, Samus WILL die. It is poison to all living creatures. We Chozo specifically made it so. But there is a chance, however slim, that Samus can survive. We must do everything in our power to ensure that she does. We can always escape from prison; we cannot get another Samus."

"One of us could be at the ready to help the rest escape once the time comes," Wesley suggested. He had woken up in the middle of the conversation, and was now sitting upright.

Odius sighed. "I still think we shouldn't risk it," he said, "but since I'm outvoted…a Federation hospital it is."

-=-=-

Rodriguez's six bodyguards assumed their positions as the ship pulled into the docking bay. Their arrival was top-secret; all precautions had been taken to ensure that nobody that wasn't involved with this business knew of it.

The door to the ship opened up, and two Space Pirates walked out, assuming positions on either side of the door. They were followed by three slow-moving figures, robed and hooded to conceal their decrepit forms. But Rodriguez was well aware of their identities.

At last, the three came before Rodriguez. "Federation President," one of them said in a trembling voice. "We have arrived as per your instructions."

"Search the ship," Rodriguez said to one of his bodyguards. "I want to be certain that there are no hidden troops or weapons."

The bodyguard nodded and moved forward, but one of the three robed figures gripped his arm with surprising strength as he passed by. "What is keeping you from taking control of our ship and taking us hostage?" he demanded. "Can't you just scan the ship to ensure that we have upheld our agreement?"

"Fine," Rodriguez snapped. "Go to the scanning room and search for energy and life signs within the ship."

The robed figure released his hold on the bodyguard, who quickly went to comply with the president's orders.

"Now, what is it that you came here for?"

The three removed their hoods, revealing their wrinkled pirate faces. "You are aware, of course, of the hierarchy of the Space Pirate society. We, alongside Ridley and Mother Brain, are at the top."

Rodriguez nodded. "Of course. The High Command."

"Yes. We recently regained control of Mother Brain, restoring the entire council of High Command once again. But then, to our shock, something unexpected occurred…"

Another of the three High Command members continued. "X Parasites were released on the newly restored Zebes, thanks to the failures of Ridley. A significant portion of our troops stationed there were infected before we managed to convey orders to the remaining troops. Then, Mother Brain herself was infected by the X."

The third one concluded the story. "They sent us an ultimatum: if we did not assist in their spread, then the X would wipe us out. We deliberated the offer for some time; we shared a common enemy, and an alliance with them would be profitable. But we decided against it; the X are too unpredictable to be a reliable ally.

"That's all well and good," Rodriguez said, "but what does this have to do with the Federation?"

A crooked smile crossed their faces. "In lieu of an alliance with the X, we are here to propose a temporary alliance with the Galactic Federation."

Rodriguez did not return the smile. "I don't trust you for the same reasons that you didn't trust the X."

"We essentially put ourselves at your mercy to deliver this message; is that not enough a sign of goodwill?"

"No," Rodriguez responded curtly.

"Very well, then. What if we were to disclose to you all of our scientific breakthroughs…including those in DNA infusion?"

That piqued Rodriguez's interest, but he was still suspicious.

"How are you aware of those experiments?" he demanded.

"I do not know what you're talking about."

"Don't try to play innocent. You specifically mentioned DNA infusion. You know about the experiments we are conducting."

The pirate sighed. "Yes, it is true. We have spies stationed in all sections of the Galactic Federation. You have our guarantee that they will be withdrawn once you accept our offer."

"And how will I know that?" Rodriguez asked. "How will I be certain that ALL of the spies have been removed?"

"Your paranoia is unfounded," the pirate said coolly. "If nothing else, the three true Space Pirates of High Command are honorable. We are willing to assist you in bringing down our common enemy, Samus Aran; we are willing to give you the research we have attempted to use to destroy you. Yet you are not willing to accept our alliance because you are unsure whether or not we speak the truth? Regardless of whether or not ALL the spies are removed, even the removal of SOME would be a huge loss to our intelligence. Think without bias, Federation President; High Command has your best interests at heart."

Rodriguez sighed, placing his thumb, index finger, and middle finger on his forehead as if he had a headache. "And what will I be obligated to do? How will you benefit from this alliance?"

"Our only request is that you assist us in bringing the X Parasite threat under control."

"Fine, then. I'll have a treaty drafted up as soon as possible."

The three pirates of High Command nodded in satisfaction. "Thank you. We will remain within our ship until you have completed the treaty."

-=-=-

"Lord Ridley…a message from the rest of High Command has just arrived…"

The draconic pirate leader swiveled his head around to glare at the poor messenger. "Well? What did they say?"

"They've…just finalized an alliance with the Galactic Federation…they've given us orders to withdraw from Zebes and to await further instruction."

Ridley was silent for a few moments as he digested this information. Then, a dark look came over him.

"No. The Space Pirate Empire shall never lower themselves to working with Federation scum. Those senile old men think that they can just order me around? WELL THEY'RE DAMN WRONG!" he roared.

"Sir, what are you…"

"I'll tell you what I'm planning," Ridley hissed, grabbing the messenger in his claw and bringing him to eye level. "I'm planning a Space Pirate Revolution. The senior members of High Command are no longer fit to rule. They must be killed if the Space Pirate Empire is to survive."

* * *

**Extra #6: High Command**

As we have already mentioned, the Space Pirate ruling body is known as High Command. It is composed of five members: Auros, Ferrix, Duma, Ridley, and Mother Brain. The former three are the senior members of High Command. They were the original founders of the Space Pirate Empire, and originally made all the decisions; however, they were forced to acknowledge Ridley's military prowess and gave him a seat in High Command. Mother Brain's intelligence earned it a seat in High Command, as well.

While all the members of High Command are supposed to be on equal footing, it is actually the senior members who hold the most sway. This is because they agree on most issues; thus, they can outvote Ridley and Mother Brain. While they might take advice from the other two at times, it is ultimately Auros, Ferrix, and Duma who make the decisions. While Mother Brain does not seem to particularly care, Ridley despises this situation.

* * *

**Extra #7: The Space Pirate Civil War**

A rift has been growing amongst the Space Pirate forces, one that threatens to tear the Empire apart. Dissatisfaction with the current government runs rampant, and it was only a matter of time before a war would break out - especially among such a bellicose species.

The release of the X Parasites on Zebes triggered the war, giving the malcontents an opportunity to break off from the main pirate force and begin building their forces. As time went on, more factions appeared, until the current four-way war that we have now became evident.

These are the warring factions in the Space Pirate Civil War:

-Those who remain loyal to High Command - or, more accurately, its senior members. They have formed a temporary alliance with the Galactic Federation to end the insurrections. They believe that Ridley remains loyal to them, but, as they will soon discover, that isn't the case at all.

-The X-Pirates, Space Pirates infected by the X Parasites. They are led by a sort of High Command of their own - the X-infected Mother Brain, and the numerous SA-X wandering Zebes. Their sole goal is to infect the universe.

-Ridley's troops. These are the Space Pirates who believe that the senior members of High Command have lost sight of what the Space Pirate Empire truly is, and believe that Ridley would make a much more capable leader. These are, for the most part, the most vicious troops the Space Pirate Empire has to offer.

-The rebels, Space Pirates who are tired of the endless war against galactic society and who just want to live in peace. This is by far the smallest faction, but there are pirates who share this viewpoint among the main army, as well, but are afraid to turn traitor. It is led by Odius, a former comrade of the deceased General Arvo...


	8. Part 8

Federation medical facilities were stationed all over the cosmos, havens for the sick and injured. For obvious reasons, they were a prime target for Space Pirate raids; thus, they were equipped with some of the best weapons technology and soldiers the Federation had to offer, save, perhaps, those at the capital. It was difficult to find a more secure location – and a place more difficult to break out of, should the need arise.

"This is our last chance to change our minds," Odius warned as the ship slowly drifted toward the hospital.

"We've already made our decision," replied Ashen Feather. "There's no turning back."

"If you say so. Anyway, there's a space skiff that you can deploy attached to the ship. You all should be able to fit in it. I'll wait here, staying in the general vicinity but out of range of scanners. I'm going to give you a transmitter; that way you'll be able to contact me at any time. No doubt, they'll lock you guys up in there once they discover who they're treating. Once you're ready to escape, just say the word and I'll do my best to help you break out."

Ashen Feather nodded as he took the transmitter. "Best of luck to us all."

Gently lifting up Samus, he and the others boarded the skiff and went off.

-=-=-

"Ridley's response has arrived," the pirate trooper reported. Ferrix turned around, as Auros and Duma were busy with the Federation president discussing the terms of the treaty. "And? Has he complied?"

"Yes, sir. He says that he is in the process of evacuating the planet as we speak."

Ferrix nodded his approval. "Very good. I will open a communications channel with him to give him further instructions. If I may," he said, nodding to the other members of High Command and the Federation president.

He strode off to the ship, but the trooper hastened to follow him. "You don't need to come with me," Ferrix pointed out.

"There's no telling when a Federation officer unaware of your purpose here will come by," the trooper countered. "You need some protection."

Ferrix frowned. "Very well."

He continued onward, and the trooper fell into place alongside him. Out of the corner of his eye, Ferrix observed the trooper. He seemed…tense. Nervous, almost. Was it out of apprehension?

As they walked, the trooper's pace slowed, until he was walking behind Ferrix rather than alongside him. At last, the ship that had carried them came into view.

Just then, Ferrix's sharp ears heard a distinctive _"click"_.

His foot instinctively flew out behind him, knocking the trooper to the ground just before the shot went off. The energy bullet hit the ceiling, leaving a blood-red mark there. A wailing siren went off after that, and Federation officers poured into the docking bay.

Ferrix observed this calmly, placing his foot over the insubordinate trooper's chest. He leaned down to pick up the energy pistol, toying with it before shooting the trooper in the head.

"Nothing happened here," he snapped to the Federation officers. "Go back to your posts. This is a Space Pirate matter."

Murmuring with confusion and suspicion, the crowd dispersed, leaving Ferrix and the dead trooper there alone.

Hoisting the corpse onto his shoulders, Ferrix entered the pirate ship. The message from Ridley was still on-screen, but Ferrix threw the carcass into the fuel-making shaft before reading it.

_To Unit 7122:_

_The revolution has begun. We are in the process of gathering troops to overthrow High Command. Here is your assignment: report to them that I've complied with their orders, to ensure that they don't suspect me. When you get the chance, try to assassinate at least one, if not all, of them. The fewer there are, the easier this revolution will be. I will be en route to the stronghold within a day; once there, I'll destroy the backup files of their minds and DNA. Glory to the New Space Pirate Empire!_

_-Lord Ridley_

Ferrix thought about the message for a few minutes. Then, he pressed the "Reply" button.

_To Lord Ridley:_

_I have successfully managed to kill Lord Ferrix…_

-=-=-

"How do you know this woman, anyway?" the doctor asked curiously as he ran the diagnostic on Samus.

"We don't," lied Wesley. "We found her adrift in space. Her suit was malfunctioning…she would have died had we not taken her in."

"And she might very well do so now, as well, if things keep going this way," mumbled the doctor. A chill came over Ashen Feather as he heard those words, and from the expressions on Wesley and White Voice's faces, the same was true of them.

"You said you were a Federation trooper, yes?" asked the doctor. Wesley nodded. "That's correct. Tarus Wesley, native of NX-816, born 2061 C.C." It was a blessing that the Federation didn't know of Wesley's betrayal yet.

The doctor straightened up, turning to face the trio. "Well, then," he said, "if that's the case, you probably know the repercussions of harboring Samus Aran."

Wesley sighed inwardly. He knew that this was coming, and had rehearsed accordingly.

"What the…Samus Aran?" he gasped in feigned surprise.

The doctor nodded grimly. "There is no doubt about it. It's Aran in the flesh."

"Will you heal her, though?" Ashen Feather prodded. "Even though she is an enemy of the Federation, you have a sworn oath to heal the sick and injured, don't you?"

The doctor nodded. "That's true. I'll do what I can for her. But I'll be contacting the authorities as soon as possible to come and seize her. You'll have to remain here as well, for the investigation."

Wesley nodded. "Of course. I wouldn't want to stand in the way of justice."

-=-=-

Six hours later, the doctor came out to speak to them. "I've done what I can," he said grimly. "Between her Chozo blood and the mixture of all the other DNA in there, it's difficult to pinpoint exactly how to cure her. There might not be an actual cure…but I've stopped the spread of whatever's transforming her."

"The Metroid DNA," Ashen Feather explained.

The doctor turned a suspicious eye to the Chozo. "And how would you know that?"

"I'm a specialist in the field," he lied. "I took my own look at her on the way here."

This answer seemed to satisfy the doctor. "Well, I managed to stop the spread of the Metroid DNA, but only through pure luck. I assume you all remember the Phazon Incident?"

"How could anyone forget it?" asked Wesley. "It's the closest the Space Pirates ever came to dominating the galaxy."

"Well, Aran herself was infected with Phazon during that time. While all Phazon may be gone, traces of its presence still remain within the living things it infected. As it turns out, these traces eradicate any DNA that tries to spread to their location. By moving the traces of Phazon to the edge of the Metroid DNA, I've prevented it from spreading any further."

"That…really is exceptionally lucky," Ashen Feather commented. White Voice nodded his agreement.

"Indeed. I've contacted the Federation capital…they're sending a squad to capture Aran as we speak. You may have to testify in court, so please be prepared for that."

With that abrupt news, the doctor left.

The trio was silent for a moment before Ashen Feather frantically took out his transmitter. "Odius! It's time! We need you here now!"

"I'll be there soon," his voice crackled out of it.

"How are we going to get Samus out, though?" Wesley asked.

"We'll just have to wing it," Ashen Feather replied. "Hopefully Odius won't take too long…"

-=-=-

_What are you doing, Samus?_

The bounty huntress rolled over onto her side, trying to ignore the pestering voice.

_Why do you still sleep?_

"Because I'm tired," Samus replied. "I'm tired of all of it."

_The universe needs you, Samus._

"The universe can handle itself," she snapped. "It's handled itself just fine without me for billions of years."

_You swore to me once that you would be the protector of the galaxy._

"That was when I was a child," Samus growled bitterly. "A stupid, naïve child."

_What changed your mind?_

Samus laughed darkly. "No matter how many times you put down one threat, another rises to take its place. The Space Pirates, Phazon, the X…it never ends. What's the point in protecting something when it'll just be destroyed by something else? Besides…another will rise to take my place. I'm sure of it."

_Who besides you could stop the X?_

Samus didn't have an answer to that.

_The X have the potential to infect the entire universe, and that is no exaggeration. If they do so, no other will ever arise to bring an end to them. You alone must do it._

"But I'm tired," Samus repeated. "I don't want to fight anymore."

_There will be ample opportunity for rest after you have done your duty._

Samus sat up, and the arms of her surrogate father embraced her. "You don't know how hard it is," she choked, tears welling up in her eyes.

_I don't,_ Old Bird conceded. _You have borne far, far too much._

"I've missed you, though," Samus added, smiling through her tears. "When I met Ashen Feather and White Voice, I asked if you were there too."

_I've missed you too. But I must let you go…you still must do your duty to the universe._

Samus nodded, wiping the tears from her eyes. "Right. The universe needs me." She took a deep breath. "But this won't be the last time I see you. I promise."

Old Bird nodded, his aged eyes smiling. "I will hold you to that promise, but only if you save the universe. Now, Samus…awaken and face your duty."

And she awoke.

* * *

"Odius! It's time! We need you here now!"

The sound of the transmitter snapped Odius out of his rest. Fumbling around for his end, he reported, "I'll be right there."

Jogging over to the controls, he considered his options. Breaking into a Federation hospital was hard enough to do, but breaking others out was suicide. How could he manage to do both…?

A wry smile crossed his face as he realized what he had to do. "Never thought I'd get a chance to do this again," he chuckled. "Let's just hope that I get this right…"

With that, he turned toward the hospital and turned the thrusters all the way up.

-=-=-

_"Do you really think this'll work?" asked Odius apprehensively._

_"No, but I don't have any other ideas. Do you?"_

_"No, sir."_

_"Great, then. Full speed ahead!"_

_Odius turned the thrusters all the way up, and his eyes blurred with the speed. Within moments, an enormous crash reverberated through the vessel, and Odius, Arvo, and the rest of the crew were launched violently from their seats._

_Odius groaned in pain, but Arvo was laughing for some reason. "That was amazing!" he howled._

_"Sir, I don't think this was the best of ideas…"_

_"It worked, did it not? We've punched straight through the wall of the outpost. All we need to do now is take out the Federation soldiers before they can call for reinforcements. GET UP, ALL OF YOU! GLORY TO THE SPACE PIRATE EMPIRE!"_

-=-=-

Suddenly, it occurred to Odius that it might be a good idea to fasten something around himself to keep himself from being grievously injured again.

Just as he tied the belt to the seat, the ship collided with the hospital and shot straight through the wall, smashing into the next wall. From the windows, wide-eyed patients stared in a combination of fear and disbelief.

"…Uh…I'm in," Odius said into the transmitter uncertainly.

"Yeah, we kind of noticed…" Wesley's voice responded.

"Well, hurry up and get in here. We don't have all the time in the world."

"There's a bit of a problem…" Wesley replied hesitantly. "We can't find Samus."

"What?" Odius demanded. "Didn't you check what room she was in when you got here?"

Federation troopers were beginning to gather around the ship. Odius swore violently. This wasn't going as planned…

"Of course we did…but she's gone."

"She must be somewhere in here. Maybe she'll come to investigate my crash?"

"We're right in the room and there's no sign of her."

Odius was silent. How could this be…?

"Fine, then. If we don't leave now, we won't be able to. I hate to leave Samus behind, but we have no choice. I'll let you three on now."

With that, he punched a button on the main console, and a force field was erected around the ship, flinging back the advancing troopers. Odius skillfully maneuvered the ship through the room (without harming anybody, miraculously), and deactivated the force field as he approached Wesley, Ashen Feather, and White Voice. He opened the hatch, hurried them into the ship, and flew out through the hole he'd come in.

"Won't they follow us?" asked Wesley fearfully. Odius shook his head. "To them, it's probably just another Space Pirate raid. Your traitor status will probably become public knowledge now, though, after associating with me…"

"We can worry about that later," Ashen Feather said. "We have more pressing matters now – namely, where Samus is."

"Shouldn't she still be back in the hospital?" Odius asked, confused.

Ashen Feather shook his head. "She was placed under constant surveillance. If she was still there, we would've known about it."

Odius sighed. "It's just one incident after another with her, isn't it…"

-=-=-

_Are you afraid?_

The voice of Old Bird resonated in Samus' mind. She smiled and shook her head. "I've never been afraid of being alone before. Why should now be any different?"

_That is good. I must go now. Take care, Hatchling._

Samus nodded and glanced down at herself. The milky white and blue hues of this new Power Suit were a sharp contrast to the red and yellow of her old one…but she liked it, nonetheless. It was lighter, yet more durable; sturdier, but more flexible. Samus did not wonder how Old Bird had given it to her; the Power Suits were just as much Chozo magic as they were technology.

The Protector's Suit, Old Bird had called it.

With that, Samus took her first few steps on her next adventure.

-=-=-

_"This isn't right, Ridley."_

_Odius held his breath, watching the exchange between the two pirate generals. This would end in bloodshed; all could see that._

_"Isn't right?" laughed the space dragon. "When have the Space Pirates ever cared about what is and isn't right?"_

_Arvo shook his head. "You're taking it too far. K-2L is a Federation planet; we don't have the authority to attack it without orders from High Command. We're only authorized to attack vessels in space; we're not allowed to land on planets and start raiding them."_

_"Listen, you idiot," snapped Ridley. "K-2L has some of the richest alfloraltite reserves in the galaxy. If we take it for ourselves, we'll have cut off one of the Federation's most important resources and bring us one step closer to winning this war. High Command won't care at that point if we slightly bent our orders."_

_"You're completely missing the point," replied Arvo. "Right now, the Federation considers us a minor nuisance at most; they're not throwing their full military might at us. If we attack K-2L, they won't be playing around anymore. And remember, Ridley, our ultimate goal is galactic domination. If we try to crush every planet at every opportunity, some of them will be made martyrs. And if martyrs are made, then the people WILL revolt."_

_"So what are you suggesting?" Ridley asked mockingly. "That one of the most reviled species in the galaxy tries to conquer it through diplomatic means? Please. Brute force is the only way we can succeed."_

_Arvo reached his hand into his gun holster, gripping it tensely. "You're making an enormous mistake."_

-=-=-

Odius stared numbly at K-2L as it passed by.

* * *

**Extra 8: The Protector's Suit**  
The Power Suit. The absolute pinnacle of Chozo technology. It is just as much a construct of their mysterious powers as it is of metal. Able to adapt with almost any technology imaginable, there are few things it cannot do. The wearer may dematerialize it at will.

The Protector's Suit is the ultimate Power Suit, the most sacred of all Chozo treasures, crafted specifically for the protector of the galaxy - who is, of course, none other than Samus Aran.

The helmet is mostly white, with two thin, symmetrical blue stripes reaching around the sides. The shoulders are completely white, smooth and featureless, about half the size of those of the Varia Suit. On the chest, there are three decent-sized blue orbs set in a triangular position. The arms have blue highlights on them, as well.

The defenses of the Protector's Suit, as one might expect, far surpass those of the Varia Suit. More importantly, though, all the powerups are built into the suit, so they can't be lost in freak accidents, as is so prone to happen to Samus. It also features a few bonus abilities, such as a second Power Beam able to be fired from the palm alongside the arm cannon. Finally, the Protector's Suit drastically increases the user's agility.

But all of these benefits only work when the protector of the galaxy herself is wearing the suit.

* * *

"Are you okay?" Wesley asked Odius, noticing the Space Pirate trembling slightly. He nodded. "I'm fine. Just…remembering something." He turned his head away from the window.

White Voice was piloting the ship, the mute Chozo's eyes unreadable. Wesley wondered what he was thinking.

"So, what's our next course of action?" asked Ashen Feather. "Do we try to find out what happened to Samus, or do we go with our original plan of traveling to Lycas in search of Metroids?"

"I think," Wesley said, "we need more information. We're still not entirely sure what the Federation's up to. I say we infiltrate the capital to see if we can find out anything."

Odius frowned. "They probably know that you're a traitor by now. You can't just waltz into one of the most heavily guarded places in the galaxy and expect to be left alone."

"I never said it'd be easy, but let's face it – we have no idea what the Federation's been up to. I'm sure we'll find a way."

"Fine, then. But I still don't see how we'll be able to infiltrate it."

"We can find a way," Ashen Feather assured them. "It may be well-defended, but I'm sure that there are a number of weaknesses."

"Hmph. What's the Federation capital like, anyway?" Odius asked, changing the subject. "I've never been there before, obviously."

Wesley shrugged. "It's basically a giant space station," he said. "About the size of your average city. It's divided into…sixteen sectors, I think. I could be wrong about the number, I never really bothered to check."

Odius nodded. "It's big…that's good. That means that when we get in there, it'll be more difficult for them to coordinate an organized attack on us."

Wesley grinned. "So you do think we can do it, after all."

"I never said that."

-=-=-

"So, that's that, then," the Federation president said. "But remember…this treaty only applies until these insurrections of yours are put down."

High Commander Auros nodded. "Of course. We…"

"Lord Auros, Lord Duma, if I may interrupt?"

The two High Commanders and the Federation president turned toward the third member of High Command in surprise. "Lord Ferrix, go ahead."

Ferrix nodded. "Thank you. You know of Lord Ridley's dissatisfactions with the current state of affairs, yes?"

Duma nodded. "Of course. As much as Lord Ridley tries to hide it from us, it is hardly a secret."

"Well, it seems that Lord Ridley has become fed up with us. He has declared himself the leader of a 'Space Pirate Revolution' and intends to overthrow us. A unit loyal to him just tried to kill me, and he is headed to our stronghold to destroy our backups as we speak. He believes that the rogue unit has succeeded in killing me…I suggest that we depart immediately and take him by surprise."

Auros turned to the Federation president. "Is our departure agreeable to you?" he asked. "We hate to depart on such short notice, but, as I'm sure you can tell, this is an emergency."

"Go ahead," Rodriguez grunted. "It's not within my power to stop you even if I wanted to."

Auros stuck out his right hand to shake it, and Rodriguez instinctively did the same. But then he remembered the Metroid DNA, and instinctively withdrew it, holding out his left hand instead. "My right wrist is in pain," he said as an excuse.

Satisfied with this answer, Auros shook his left hand instead. Duma and Ferrix did the same, and High Command departed.

Rodriguez sighed. He needed some rest.

-=-=-

The icy wastelands that stretched out in front of her reminded Samus Aran of the Phendrana Drifts. In her line of work, you saw a lot of incredible sights, but the serene, freezing beauty of Phendrana remained her favorite by far.

She felt a faint presence emanating from across the ice, and she knew that she wasn't far from her destination. Another few hours and she'd reach it.

She toyed with the trigger in her arm cannon apprehensively. It wouldn't be that easy, though. It was never that easy.

Shrugging, she continued onward as the presence grew stronger.

-=-=-

"We're getting close," Wesley reported. He could tell thanks to the increasingly heavy traffic around them.

"How many docking bays are there?" asked Ashen Feather curiously. "About 100," replied Wesley. "But I don't think we should use any of them…as soon as they asked for our identities, we'd be caught."

"So, do you want me to repeat that stunt I pulled back at the hospital instead?" Odius asked dryly. Wesley shook his head. "No, I think that'll put us in an even worse position. I have an idea, though…"

He thought back to when he was first entangled in this mess. It was stupid, crazy…but it had worked for Samus, so…

"Hail a ship," Wesley said. "Preferably a trading vessel."

White Voice nodded and did as he was told. He established a communications channel between their ship and a nearby trading vessel.

"What is it?" a gruff voice grunted.

"This is the Galactic Federation Bureau of Illegal Activities. We believe you to be smuggling illegally acquired goods from the Federation. Please allow us to board your ship in order to perform a search." Wesley thought it to be a good lie, if he said so himself.

"Yeah, I'll just do that…" the voice replied.

Suddenly, the ship sped off, erratically changing directions.

"YOU'LL NEVER CATCH ME!" the man in the ship shouted.

"…I guess he really was smuggling illegal goods…" Wesley commented in surprise. Moments later, the other's ship crashed into another nearby ship.

"…Second time's the charm?" offered Odius.

"Hopefully," Wesley replied as Ashen Feather tried again.

-=-=-

"Sir?"

"What is it?" Rodriguez grumbled sleepily.

"I hate to wake you up, sir, but this is urgent. We had Samus Aran in our custody."

Rodriguez sat up, alarmed. "Aran? You've found her?"

"_Had_, sir."

The Federation president stared at the messenger in disbelief. "You let her go?!"

"No, sir. She escaped on her own."

This news was maddening to Rodriguez. "Why wasn't the security stronger?" he demanded.

"It was the strongest we could make it…I don't know how, but she escaped. It was like she'd never been there…nobody saw her do it."

Rodriguez couldn't think straight, for some reason. "Fine. Fine. You know what? Fine. I know how I can handle this. Should've just done it from the start." He was talking to himself more than he was to the messenger.

"Sir? Are you okay?"

"Fine. I'm fine. Everything's perfectly fine." He glanced down at his glove-covered hand nervously.

"Please leave me alone."

The messenger nodded and departed, wondering what was wrong with the president.

"Aran hates those experiments of mine, does she?" Rodriguez mumbled feverishly to himself. "Then let's give her an opportunity to destroy them."

He laughed deliriously, finding the idea absolutely hilarious for some strange reason.


	9. Part 9

"This is the Galactic Federation Bureau of Illegal Activities. We believe you to be smuggling illegally acquired goods from the Federation. Please allow us to board your ship in order to perform a search," Wesley repeated, hoping that the ship he was contacting was innocent this time.

"Uh, okay…" was the response. The other ship slowed to a stop, and their ship pulled up alongside it. Wesley stepped through the hatch into it. "What's your name, sir?" he asked the victim of his trick.

"Patrick Halbruner," responded the confused trader. He started toward the cargo hold. "All the stuff I'm carrying is in here, I'm sure you won't find anything…ob…jection…able…?"

He trailed off as he noticed the gun aimed at him.

"Don't move," commanded Wesley as Odius, Ashen Feather, and White Voice filed into the ship. "Tell us where all your pieces of identification are."

"In the glove compartment," Patrick responded with fear. Wesley gestured for Odius to check, and they found all the necessary papers where he had said.

"Now, listen carefully," Wesley said. "We're going to take this ship. You can take ours in exchange; it's a better one, anyway. When we get the chance, we'll find you and send your identification papers back, along with ten thousand credits, provided you don't turn us in. Does that sound good to you?"

Patrick nodded silently.

"Good. We hate to do this, but we have no choice. Now get out of here."

Nodding, the man quickly scurried through the hatch into their former ship and flew off.

"That went well," said Wesley cheerfully. "Now we can dock at the capital without any suspicion." He glanced at Odius. "Not entirely sure what we can do about you, though…"

The Space Pirate shrugged. "I'll be content to wait out of sight in the cargo hold if I have to," he said.

"That solves that problem," said Wesley. "So let's get to it."

-=-=-

"President Rodriguez, sir?"

"Now what?" he snapped. Moments before, he had been perfectly cheerful, but now he was irritated beyond belief. For the past few hours, he had been subject to these mood swings…he wished he knew why.

"Status update on the X project, sir. We've successfully eliminated their weakness to Metroids. Even more, they seem to be completely under our control."

"Send them after Aran," Rodriguez replied immediately.

"…Um, sir…we don't know where Aran is."

Rodriguez glared at the man. "Do I look like I care? If you can't find Aran, then draw her to us. Deploy the X Parasites on a place that's important to Aran. Tallon IV should suffice."

"So you want them deployed on Tallon IV?"  
"That's what I just said, isn't it?"  
"Point taken, sir."

As the man departed, Rodriguez's cheerful mood returned. He took off his glove and toyed with the claws on his hands.

-=-=-

They had gotten into the Federation capital without any problems. After docking, Wesley had assumed the identity of Patrick Halbruner, pretending that Ashen Feather and White Voice were unregistered with the Federation. Now, they wandered Sector 11, searching for information about the Federation's recent activities.

"Sectors 10 through 16 are open to the public," Wesley explained to the two Chozo as they walked. "I know a guy who can get us into the other ones, though."

With that, he led them down one hall. "Sectors 10, 11, and 12 are for government-related things. Sectors 13, 14, 15, and 16 are on the rooftop; they're the capital's city. The guy I'm taking you to is in Sector 15."

They arrived at an elevator, and Wesley pushed the button marked "15".

Once they reached their destination, Ashen Feather and White Voice gaped in awe at the sight that spread out before them. The Federation capital city was the pinnacle of Federation society. Countless skyscrapers reached toward the artificial atmosphere, with even more countless people milling about.

"Impressive, isn't it," said Wesley. "The Federation can build a great city, if nothing else."

With that, he led them down one road, into one of the less flattering parts of the city. At last, they arrived at a small restaurant, which Wesley led them into.

Except for a reptilian man cleaning dishes at the counter, the restaurant was empty. He glanced up as they walked in, and his eyes widened in surprise.

"Tarus? That you?"

Wesley nodded. "Surprised to see me?"

The restaurant owner grinned. "Not really. Traitor or not, you always find your way back here. But who're your friends?"

"These are Ashen Feather and White Voice of the Chozo. Guys, this is Daalin, of the Arbezt."

"Pleased to meet you," Daalin said, giving them a toothy grin.

"Daalin's a retired army officer," Wesley explained. "He's made a lot of friends among the higher ups in the Federation, so he can get us into the private sectors."

Daalin's grin faded. "'Fraid not, Tarus. My buddies are under extra-strict orders not to let anyone into the private sectors, no matter who asks. I can't help you there."

Wesley frowned. "Well, do you at least know what's been going on in the Federation?"

Daalin hesitated. "…Yeah, I know that. But it wouldn't be good for anyone to hear me talking about it…if we head into the back room, it should be fine…"

He walked around the counter, and switched the sign on the window to say "Closed". He gestured for them to follow him.

"All right," he said after closing the door to the back room. "What do you want to know?"

"What's the Federation been up to?" Wesley demanded. "What are they trying to hide the most?"

Daalin stared at Wesley in surprise. "You've never been this suspicious before," he commented. "In fact…you seem…never mind," he muttered.

"Well, let's see…where to begin, where to begin…there's a lot that even I'm not privy to, but from my understanding, the Federation's recently formed a new alliance of some sort…apparently, it'd be controversial if the details of the alliance were leaked to the public, but that's all I know on that issue. Uh…something big also went down in Sector 7…apparently big enough for them to completely shut it off to everyone. They've been conducting experiments of some sort in there since then…"

"Anything else?" asked Wesley.

Daalin shook his head. "Sorry, that's all I know. Aside from the usual government business, anyway, and you know how that is."

Wesley sighed. "I was hoping for some more concrete information, but thanks anyway."

A thoughtful expression crossed Daalin's face. "Well…there is one last thing of interest. I don't know if it's what you're looking for, but it might help you, regardless."

He reached up onto a shelf and brought out a small, slightly dated computer. "From time to time I'm given access to the Federation's main database," he said. "The last time I was allowed to do that was a few weeks ago, and I found something interesting in there…"

"What was it?" asked Wesley

"A dormant AI," replied Daalin. "It was hidden amongst unimportant files, so I assumed that it didn't want to be found. I transferred it to this computer and activated it, but it's refused to communicate with me…"

"Maybe we'll have better luck," suggested Wesley. "Let's try and see."

Daalin activated it, and a circle appeared on-screen.

"…YOU!" it roared upon seeing Wesley.

Wesley took a step back uncertainly.

"What have you done with Samus?!" the computer demanded intensely. At this, Ashen Feather began paying attention.

Wesley's eyes widened as he realized what the AI was. "Adam!" he exclaimed in relief.

"Answer the question," Adam snapped.

"We've done nothing with Samus," Ashen Feather interjected. "We're her allies. She disappeared, though, and now we're trying to find her."

"You betrayed Samus, though," Adam growled to Wesley.

"I wish I hadn't," Wesley said quietly. "But what's done is done. I am now completely on Samus' side. And if you don't believe me, well…you can ask Samus herself once we find her. But I'm just wondering…how are you still intact? I thought you'd been retooled into a Federation AI?"

"Samus told me to copy myself to the Federation mainframe before they had finished retooling me," Adam replied. "I remained dormant there until this person came."

"Wait," said Ashen Feather. "If you were on the Federation mainframe, then did you manage to find out what they were up to?"

"I still _am_ connected to the mainframe. But if I make any activity on there, then they'll be able to detect me and find you."

"That's fine," said Wesley. "We can wait until we're a safe distance away from the capital to find everything out."

Wesley turned to Daalin. "Thanks for everything," he said.

Daalin grinned. "My pleasure."

-=-=-

On the planet Tallon IV, above the icy Phendrana Drifts, a Federation ship passed above. Its cargo doors open, and countless yellow, amorphous blobs descended on the landscape…

* * *

"Do you think we're far enough away yet?" asked Odius, peering at the Federation capital rapidly shrinking into the distance.

"Probably," Wesley considered, "but let's keep going for a few more minutes just to be safe."

With the safe recovery of Adam, they had left the Federation capital in good spirits. They had uploaded him to their captured ship, and now they were preparing to put the plan into action. Their plan was to have the computer find some helpful information, then quickly disconnect and escape before the Federation could detect Adam and track them. It was risky, but they were confident it would work if they were far enough away.

"Right, that should be good enough. Adam, you know what to do."

"Of course."

There was silence for a few moments until Adam spoke once again.

"Mission accomplished. I could only gather one bit of information before they would detect me, but it's helpful, nonetheless. Take a look…"

The hologram of a yellow blob appeared on the display. "That's an X Parasite!" gasped Ashen Feather.

"Precisely. The Federation got its hands on a good amount of them and has been conducting experiments to further their potential as a biological weapon. Some of them were deployed on Tallon IV just a few hours ago, in fact."

"Why Tallon IV?" Odius asked, confused.

"That information isn't in here, unfortunately."

"We need to find Samus, then," muttered Wesley. "We need her to defeat the X. There are no other options."

"I should be able to find her," Adam offered. "I have a link to her suit, and…"

White Voice held up Samus' disassembled Power Suit.

"…Oh."

"Even if she did still have her Power Suit," Ashen Feather said, "she's disconnected her link to you. The Federation could find her at any time thanks to that retooled version of you. We don't have any way to reach her."

-=-=-

The guard sighed and let out a puff of smoke from his cigarette. This job was pointless, if you asked him…aside from himself, the other guard, and the half-dozen or so scientists in the building they were guarding, there was no life on this planet. What did they need protection from?

"Hey, Bill," his buddy said.

"What?"  
"Did you see that?"  
"See what?"  
"That. Right there."

Bill squinted into the distance, trying to see what his fellow guard was pointing to. "I don't see anything."

"There was somethin' jumpin' around. Like a human bunny or somethin'."

"You're hallucinating, Rob," Bill snorted. "Ain't nothing around here but us, the snow, and the mountains."

"I'm tellin' you, it was -"

"It was nothing," repeated Bill. "You're just seeing things 'cause you're bored like I am. 'Cept I'm not loony like you."

"If you say so," Rob said uncertainly.

"I do say so," Bill replied. "And don't you forget it."

"How long we got left on this shift, anyway?" the second guard asked, trying to change the subject.

"Two weeks, I think. Then another two bums are gonna come down here and have to stare at the snow for a month." Bill spat on the ground as if to enforce his point.

"What could they be doing in there, anyway?"

"Dunno. Don't care."

Suddenly, the door opened behind them, and one of the pudgy-faced scientists poked his head out. "Dinner's ready," he reported. "You two want to come inside?"

The guards nodded, and they contentedly walked through the door.

Samus Aran watched them go from behind one of the snow dunes.

-=-=-

No doubt about it, now: this was the place she'd been looking for.

The presences within the building were beginning to give Samus goosebumps, they were so powerful. Old Bird had assured her that they wouldn't attack her, but she couldn't help but feel somewhat frightened at the prospect…after all, every other time she had faced them, they'd been trying to kill her.

…Except for once, she considered.

Samus shrugged. She'd worry about that when she got there. For now, she needed to consider her course of action. Did the Federation contact this facility often? If so, forcing the residents out would make it obvious that something was wrong…but if they were allowed to stay, they could give her away at any time…

_I'll just get in and out of there as quickly as possible,_ Samus decided. With that, she started down toward the building, prepared to fulfill her purpose here.

-=-=-

A crash resounded through the whole facility, shaking its very foundation. Bill dropped his fork. "What da hell wash DAT?" he demanded, his mouth still full of food.

"I'll go check," offered Rob. He got up from his seat and walked in the direction of the crash. Thirty seconds later, he rushed back, his eyes wide with fear. "Samus Aran!" he cried. "It's Samus Aran! That's who I saw earlier!"

"Go fight her," one of the scientists commanded.

Bill stared at him. "What are you, nuts? She'll kill us without breaking a sweat!"

"Anyone else want to try fighting her?" the scientist asked. Nobody raised their hand.

"Alrighty, then," he said, and they all went back to eating their dinner.

-=-=-

Samus was surprised at the lack of pursuit, at first, but didn't bother questioning it. She walked unchallenged into the heart of the facility, and shivered in spite of herself. She had known what to expect, but it didn't make actually seeing it any less unpleasant.

Metroids.

Almost every stage of them, from baby to Zeta. Samus assumed that they hadn't discovered how to control Omega Metroids yet, but she didn't care; her last encounter with an Omega Metroid had been less than pleasant, anyway.

There were two or three of each, held in frost-encrusted stasis tubes. After a bit of hesitation, Samus fired a missile at a tank containing at Alpha Metroid. As the tube shattered, the Metroid let out a shriek and flew at Samus. The bounty hunter prepared for trouble and leveled her arm cannon at the beast before it paused. Then it floated calmly over to Samus and stared at her expectantly.

Samus reached out with her hand apprehensively and pet the Metroid. It let out a trill of happiness in response.

"…Wow," Samus murmured, and continued to free the rest of the Metroids.

Before long, all ten of them were gathered around Samus. She was shocked; not a single one of them had showed any sign of aggression towards her, aside from some anger at the beginning, which she assumed was from being trapped for so long rather than directed at her.

Strangely enough, she felt a sort of kinship with them.

"Right, then…" she muttered. "Let's get you guys out of here."

She spotted a communications unit, and walked over to it. She tried to remember the contact code that Ashen Feather had given to her on Zebes.

-=-=-

A beeping sound rang out from Ashen Feather's pocket. He took the portable communicator out in shock, staring at it.

"…It says that it's from a Federation facility," he said fearfully. "But the only person I gave it to was Samus…"

"Did they capture her after all?" wondered Wesley.

"Answer it," urged Adam.

Ashen Feather pressed the button nervously. "Hello?"

"Ashen Feather? Is that you?"

"Samus? Oh, thank heavens you're alive!"

"Listen, I'm in a bit of a fix here. I'm stuck on the planet Lycas in a Federation facility with some…er, friends. Could you head down there and get us?"

"What the…Lycas? How in the cosmos did you get there?"

"Long story short? I had a little help from your people…"

Ashen Feather blinked. "You are a woman of many surprises, Samus."

* * *

Samus sat at the table, staring uncomfortably at the facility's staff on the other side. They were all too aware of the powerful arm cannon resting on the tabletop. That, and the ten bloodthirsty Metroids all around them that they had imprisoned.

Gradually, the sound of a ship engine became apparent, and something landed by the facility. "That must be my ride," Samus said. She got up. "Sorry for all the trouble, but I do what I need to do. You can understand, right?"

They couldn't, but in order to appease the dangerous bounty hunter they nodded. Samus led the Metroids out to the snowfields, where the ship was waiting.

Ashen Feather was waited outside. When he saw Samus' new suit, his jaw dropped; when he saw the ten Metroids, the color drained from his face. "You've got a LOT of explaining to do," he muttered as they headed back into the ship.

Samus grinned. "I thought you might say that."

"We're going to need a bigger ship," Odius grunted as their ten extra guests filed in, forcing them all to remain squeezed together.

"Just throw everything unnecessary out of the cargo hold and keep them in there, they're used to being in tight spaces anyway," Samus replied.

"They're not gonna eat me, are they?" Wesley asked, eyeing the Metroids fearfully.

"Probably not."

"_Probably_ not?" Wesley repeated, his eyes bulging with fright.

"All right, Samus," Ashen Feather said. "Please tell us what in the name of the cosmos is going on here."

Samus sighed. "Old Bird – my surrogate father," she added, noticing the confusion from Odius and Wesley, "visited me while I was unconscious. To keep things brief, he brought me here and gave me this Protector's Suit as a replacement for my old Power Suit – you guys still have that, right?"

White Voice held up the helmet in confirmation. Samus nodded her satisfaction. "Good. Well, he told me that the Federation was conducting Metroid experiments on this planet, and that if I freed them they would make valuable allies. I did as he said, and, well…here I am. So, what have you four been up to while I was gone?"

"Five, actually, lady."

Samus whipped around in disbelief, staring at the shipboard computer. "Adam?!" she cried.

"The one and only."

She turned back to Ashen Feather. "You've got a LOT of explaining to do," she said, echoing his earlier words.

As they retold their story, Samus seemed to be deep in thought. Every now and then, she would glance back at either Adam or the Metroids.

"…and thanks to him, we found out that the Federation has sent the X Parasites to Tallon IV. We don't know why, but with you and all these Metroids, we can get rid of them before they grow to be a threat…!"

Samus frowned. "No, we can't."

Ashen Feather blinked. "But, why…?"

"They're trying to lure me there," Samus muttered. "They're trying to force me out of hiding by attacking a place dear to me. There's no other reason for them to go after Tallon IV…"

"Then…what do we do now?" asked Odius.

Samus thought about this for a moment. "We do the same thing they're doing," she decided. "We need to draw them out. We need to get them to fight on our terms."

She deliberated for a few more seconds. "We will return to Zebes," she said. "We won't hide our activities, either; the more people who know where we're going the better. They will need to decide if attempting to follow me onto one of the most dangerous planets in the galaxy is worth it or not. In the meantime, we can focus on purging Zebes of the X."

Ashen Feather eyed her skeptically. "Eleven individuals won't be able to completely purge a whole planet's worth of them, you know."

"That's true," Samus agreed. "But we can do what we can to slow it down. And besides…there's something there I want to do…" she added, images of a robotic brain exploding from a Super Missile in her head.

"What about the rest of us, though?" Wesley asked. "I'm definitely not going down there again. You're the only one of us who won't get infected."

"Your job," Samus said, "is to help Odius." She turned to the surprised Space Pirate. "I promised that I would help you bring down the Space Pirate Empire, and so far I haven't kept that promise. Under these circumstances, this is the best I can do."

"I understand," Odius replied, shaking Samus' hand.

Odius now turned to the rest of them. "Here is our plan of action," he said. "After we've dropped off Samus and the Metroids at Zebes, we'll meet back up with my troops. They've been given orders to find out what the rest of the Space Pirates have been up to. Once we know everything we need, we'll plan out the rest from there."

Everyone else nodded their approval. "Good, then," Samus said. "Adam, set us on a course for Zebes."

"…This ship doesn't have any way for the computer to control the travel either, lady," the computer said dryly.

"Oh. Okay, then…one of you set us on a course for Zebes."

White Voice stepped forth to do as Samus requested.

-=-=-

President Rodriguez was in exceptionally poor condition. He was continuously trembling, on account of the freezing weather (the Federation capital was heated to a temperature of 70° Fahrenheit). He kept muttering to himself deliriously, and looking around as if in search of somebody watching him. He refused to be inspected by doctors, though; he insisted that he was fine and that everything should be carried out as normal.

The messenger (who, in recent days, had taken a keen dislike to the president, thanks to his behavior) poked his head into the office again. "Sir…another update on Samus Aran," he said distastefully.

"Aran?" the president asked excitedly. "Did you catch her? Is she dead? What? What is it?"

"She's been spotted on numerous planets in the past few hours. In all cases, she's been quoted as saying that she's headed to Zebes."

"Zebes, eh?" Rodriguez muttered. "She must be trying to lose me…must be trying to escape my grasp by fleeing to the planet she thinks she's safe on…fine then. I know just what I'll do."

He glanced up at the messenger. "Prepare my ship," he ordered. "Inform the GFS Valhalla that I'll be arriving soon to take all their experiments for a field test."

The messenger nodded, seeing what Rodriguez was planning. "With any luck, he'll die in the attempt…" he mumbled to himself.


	10. Part 10

**FINALE - PART 1**

"Right there," Samus said, pointing out the window. "That's a good spot."

White Voice obliged, lowering the ship to the place Samus had pointed to. It was a short distance from the entrance to Crateria's caves.

Samus stepped down from the ship, the Metroids following suit. "I'll see you all again soon," she promised them.

"Don't you dare think that you can leave me behind again," a voice in her helmet reprimanded her. Samus was startled for a moment before a smile crossed her face. "I'd never dream of it, Adam."

Samus waved good-bye to her allies as they departed, then turned around and started walking in the direction of the caves, five Metroids flanking her on either side.

X Parasites swarmed all around her, but kept their distance for obvious reasons. Though the Metroids seemed eager to feed on all the prey flying around, Samus' authority seemed to keep them at bay. As much as she would love to get rid of as many X Parasites as possible, she was determined not to stray from her main purpose.

She wondered, suddenly, if the Mother Brain itself had been infected by the X Parasites. She dismissed the thought immediately. It was not a mere possibility; it was practically a given fact. When she had left Zebes, the X were already in Tourian. Mother Brain's defenses were potent, but not nearly potent enough to repel an endless wave of them. It would only take one X slipping by its defenses to completely infect it.

That was why the X were so dangerous, Samus reflected. A single one escaping (thanks to her, no less) had utterly destroyed this planet's ecosystem. One little X Parasite could become one million in a matter of days.

As they entered the endless tunnels of Zebes, Adam seemed to become restless. "Samus," he said, "you do know what's following you…right?"

Samus nodded. "I know. I know."

Her eyes were swiveling to and fro in search of this unseen stalker.

"There's more than one of them, though. They're all camouflaged somehow…they couldn't do that back on the B.S.L…"

"They probably mutated to obtain that power. You know how volatile the X are, Adam."

"Right…well, I just thought I'd warn you, lady."

"Don't worry about me. I know what I'm doing."

Samus' eyes caught a distortion in the air before long, moving at about her pace. "There's one…" she mumbled under her breath.

She stopped, suddenly. The Metroids paused as well, confused. Samus raised her left hand, pointing the palm at the distortion in the air. A violent blast erupted from it, smashing into the now visible SA-X and sending it careening into the wall. A pile of debris tumbled down on it, and it was still.

All around them, now, eight more SA-X disabled their camouflage, forming a circle around the real Samus and the ten Metroids. The bounty huntress was shocked; she hadn't expected this many of them…

Tapping into the Metroid DNA within her, Samus communicated her intentions to the Metroids. She hated to do this, but she had no choice…with any luck, they'd be able to handle this on their own…

The Metroids seemed to approve of her plan, so Samus leapt into action.

Literally.

Leaping over the heads of the SA-X, Samus began rushing in the direction of the elevator to Tourian. Out of the corner of her eye, she saw one of the SA-X abandoning the others to follow her. That was good; she had been expecting that. Plus, it would take some of the burden off of the Metroids, as well…

"All right, then…" Samus muttered. "Let's see how well you can keep up."

Samus abruptly turned a corner, the Protector's Suit aiding in keeping her movements fluid. The SA-X, not expecting this, screeched to a halt before racing after Samus again.

Samus knew the corridors of Zebes like the back of her hand; she had all but memorized them during her numerous trips to the planet. She doubted that even the Mother Brain itself knew them as well as she did.

Noting the weak floor ahead of her, Samus waited until she was just on the edge of it before leaping into the air and Space Jumping across it. The SA-X was not so lucky; it ran straight onto it, and the weak floor crumbled beneath it. But the SA-X's swift reflexes saved it, as it jumped just before the floor disappeared entirely.

The elevator to Tourian was swiftly approaching. Once Samus reached it, she was in the clear…the SA-X would have to wait for the elevator to bring Samus down, then wait for it to go back up again…and by the time that happened, Samus would be long gone.

At last, the hatch came into sight. Samus leveled her arm cannon at it and fired off a shot. The blue doors opened, and she rushed through them. The familiar pink platform greeted her, and she quickly activated it. The elevator slowly began to descend just as the SA-X came into the room.

It stared down the elevator shaft, its blank eyes meeting Samus'. Then, it leveled its arm cannon and fired at her.

Much to Samus' relief, though, the nature of the Wave Beam caused it to split apart just as it reached her, passing harmlessly through her. Her relief was short-lived, though, as it instead cut straight through the platform she was standing on. It screeched along the walls for a second before falling into the abyss. Samus helplessly grabbed at the walls for a handhold before she began to fall as well.

Then, the SA-X leapt down the shaft after her.

Immediately, it fired off a volley of missiles. Most of them hit the walls before reaching Samus, but a few slammed into her, sending her spinning into the walls. Jets on her suit righted her position, as well as briefly slowing her descent. Samus aimed both her arm cannon and her palm at the SA-X, letting loose a powerful discharge of energy from each. The SA-X went head-over-heels, spinning wildly in midair.

"Adam!" Samus gasped, finally catching her breath. "Tell me when we're about to hit the ground!"

"Should I just say 'now'?"

"Yes!"

"NOW!"

Samus desperately tried to twist herself into a landing position, but the floor didn't wait for her to finish. Thankfully, her armor absorbed most of the impact, so she was relatively unharmed.

Seeing the SA-X about to hit the ground as well, Samus quickly rolled out of the way before it landed on her.

As the doppelganger slammed into the floor, Samus got to her knees and placed her palm over its visor. With as much energy as she could muster, she unleashed a powerful discharge, shattering the visor and torching the face within. An inhuman wail came forth from the SA-X, and Samus pushed the creature over the edge of the platform they were on into the lava.

"Masterfully done," Adam complimented her. Samus grinned tiredly. "Thank you."

She got to her feet and turned toward the next door. "But now comes the hard part."

* * *

Samus glanced around apprehensively as she entered the next room, prepared to make her way through Mother Brain's numerous defense systems. To her surprise, though, no turrets nor Rinka launchers met her view; just a straight corridor.

More disconcerted by this sight than she was comforted, Samus continued onward, noting the eerie silence of Tourian. Not even the hum of machinery graced her ears.

"Samus Aran."

The bounty hunter leapt up in surprise. She lifted her arm cannon and searched for the source of the voice.

"You are Samus Aran."

It was Mother Brain's avatar, floating erratically through the air. Its eye was flickering strangely.

"We have been waiting for you…Samus Aran."

"Waiting for me?" Samus echoed.

"Please come with us," was the only reply the floating eye offered. With that, it began floating in the direction of the main body of Mother Brain.

"I don't like this," Adam commented. "It's clearly a trap. We should head back now."

Samus shook her head. "No, I want to see where this is going. And besides…I can handle whatever it throws at me." Adam was skeptical, but he allowed Samus to proceed.

As they continued through the corridors of Tourian, Samus began to notice things; yellow fluid oozing out of pipes, a perpetual slushing sound, among others. It was clear that the X had taken complete control of this area.

"We await," Mother Brain's avatar said simply as they reached the door leading to its chamber.

Samus nodded and entered.

There sat Mother Brain within its tube – or at least, what remained of it. The glass casing containing the supercomputer had been shattered, exposing it to the open air. While its appearance remained mostly unchanged, a yellow film seemed to ooze out of some of its folds and crevices. As its eye opened to see the bounty huntress, Samus noticed that its pupil had turned yellow, as well. She stepped forward hesitantly.

"Mother Brain," she called out to it. "You should know why I'm here."

_"We are fully aware of your purpose in coming here,"_ it replied. _"But we are no longer Mother Brain. We are now the mind of the X. Our purpose is to spread our influence through the cosmos."_

The yellow film began to ooze out of the crevices, covering the Mother Brain with splotches.

_"We are X-Brain. We are the head; the SA-X, the arms; and the rest of us, the legs. Together, we create a perfect body that will rule the universe."_

"Your arms have been amputated, then," Samus retaliated. "I've beaten one of the SA-X, and I'm sure that the others will soon follow suit – if they haven't already."

_"More can be made,"_ the X-Brain responded dismissively.

"Then my only option is to decapitate this body of yours, then," Samus shot back coldly.

_"Bold words, Samus Aran. You'd do well to still your tongue before we lose our temper. For we led you here not to fight, but to ask you a question."_

"A…question…?" Samus repeated in surprise.

_"Yes, a question. Why do you resist us? Look around at your enemies. Your type of life continually wars with itself. It tries to impose its own rule upon others, but those others will strike back at them. With us, there will be none of this; once we are supreme, there will be no wars, no insurrections, no corruption. Only peace. So why do you resist?"_

Samus smiled sadly. "That's a question I don't have the answer to," she replied curtly.

_"Then our point is proven."_

Samus held up a finger. "Just one moment, now. Just because I don't have the answer doesn't mean that I proved your point. Because that's _my_ point; we don't always know the answer to why we do what we do. Maybe your type of existence is better; maybe not. I don't know, but I don't really care, either. I resist you because that's what I think is right. I don't know why that is. A universe without war or corruption sounds wonderful…but in the end, I will fight for my right to a universe with war and corruption."

_"You condemn our activities as evil, yet you profess to desire violence and strife in the universe?"_

"If there is nothing to strive for, then there is no reason to exist. I strive to bring about the end of confict; in order to do that, there must be a conflict. I may never accomplish my goal…but perhaps I will at least have moved the universe in the right direction in my efforts."

_"Is that your reason, then?"_ asked the X-Brain.

Samus shrugged. "Perhaps. Perhaps not."

_"That is…an intriguing response. You may now depart."_

Samus held up her arm cannon. "Now wait a minute. You may not have summoned me here to fight…but I came here with a single purpose in mind: to destroy you. I will not leave until I've done what I came here to do."

_"You are a fool, Samus Aran. A wise fool, perhaps, but nonetheless a fool. We give you the opportunity to leave this place unharmed…and instead, you choose death."_

With those final words, the Zebetites, normally stored above the Mother Brain, descended from the ceiling to block Samus' path. Most of the floor retracted, leaving only a few small platforms for Samus to stand on, and lava began rising up from beneath.

"Now that's more like it," Samus said.

As the turrets emerged all around her, she fired off a dozen missiles at the first Zebetite, destroying it before the Mother Brain got a chance to attack. She flew through the opening, eyes scanning the chamber for the locations of the turrets. As her attention was diverted, though, one of them hit her, sending her into the roiling lava. Even the Protector's Suit wasn't strong enough to withstand material at so high a temperature, and Samus began to sweat copiously. She quickly leapt out of the lava, but noticeably worse for wear.

Jumping, dodging, weaving, and moving in ways Samus never thought possible, she slowly but surely wore down the next Zebetite, regardless of its regenerative properties. The relentless onslaught of turret fire was weakening her, but she persisted. At last, the second Zebetite exploded, clearing the way to the next.

Rinka launchers now accompanied the turrets, their larger projectiles occasionally forcing Samus to jump into the turret fire instead to dodge them. To make matters worse, this particular Zebetite was partially shielded, leaving only its top and bottom exposed. She was forced to absorb some of the turret and Rinka fire in order to destroy the next Zebetite. Even as she rolled into her morph ball form to squeeze through the small hole the destroyed Zebetite left, she was hit by a Rinka.

But now, she had reached the X-Brain. Not pausing to celebrate her accomplishment, though, Samus instantaneously fired off a volley of missiles into its eye, all the while dodging the Rinka and turret fire. As she landed on the platform again, though, the X-Brain fired off eight lasers at each corner of the room, then swept them together. Samus' arm was hit with one, and as it moved she was dragged to the center and hit with all eight of them combined.

"That's a new one…" Samus mumbled, her arm burning with pain.

As she struggled to her feet, the X-Brain fired a wave of energy, smashing her into the wall behind her. She fell directly into the lava yet again.

Rapidly coming to her senses, Samus leapt back onto the platform, firing another volley of Super Missiles, along with a discharge of energy from her palm. Both hit the X-Brain head-on, and a yellow pus-like substance dripped out (melted X, Samus assumed). In response, it shot a laser that ricocheted around the chamber, adding yet another hazard to Samus' long list of them.

Samus, in desperation, rolled up into her morph ball form to make herself a smaller target. Leaping toward the X-Brain with the Springball, she left behind a Power Bomb before, somehow, completely reversing her direction in midair and returning to the platform.

As the Power Bomb exploded, the machinery within its blast radius malfunctioned and exploded, as well. The X-Brain was sent flying into the wall, then fell to the ground. It lay there, quivering, as the lava receded.

"You did it!" Adam celebrated. Samus shook her head. "No…it's not finished yet."

As if on cue, countless X Parasites flew out of the X-Brain and began to lift it up. Something began to form beneath it.

-=-=-

"Here I am, Aran!" Rodriguez cackled madly as he stepped out of his ship onto the Zebesian soil. "Come and find me! My friends and I will be waiting for you!" He laughed again as he pulled out his gun, firing back into his ship at all the stasis tubes containing his experiments.

After he had done, he stared at his hand again giddily, gaping with fascination as he witnessed the spread of the Metroid DNA.

"I wonder if there's any way to make it faster…?" he asked aloud.

* * *

Images of Samus' last battle with Mother Brain filled her head, and she began to wonder whether or not she could defeat the X-Brain. There was no infant Metroid to help her this time…there were the Metroids she had helped to rescue, of course, but even if they were still alive, there was no telling whether or not they would come to her rescue.

She was on her own.

At last, Samus' worst fears were confirmed; the familiar bipedal, bird-like body formed beneath the X-Brain, towering above the brave bounty huntress. A mouth opened up, and it screamed at Samus.

"Don't worry, Samus," Adam assured her. "You've fought worse."

Samus nodded distantly and leapt into action. She back-flipped into a wall and launched herself off, aiming in the direction of the X-Brain. The beast screamed again, and a stream of energy orbs launched themselves at Samus. The armor-clad warrior fired off a charged shot from her arm cannon which tore through the X-Brain's attack before connecting with the X-Brain itself, rending its fleshy membrane. A satisfying howl of pain issued forth from it.

Enraged, the X-Brain brought forth a bomb and tossed it at Samus. She tried twisting in midair to avoid it, but it collided with her, smashing her into the ground with itself. As it exploded, a gooey substance covered Samus, making her movements sluggish.

Satisfied with itself, the X-Brain now began gathering energy around its eye. With horror, Samus recognized this attack and struggled to escape. Desperately, she tried to Screw Attack out of the slime, but to no avail.

The X-Brain fired.

As that white wave of energy hit, Samus screamed in pain. The sludge evaporated, and she was forced back to the wall, pinned against it. Every nerve in her body was crying out in protest, begging for the torture to stop. Nearly ten seconds of utter agony later, the beam dissipated, and Samus collapsed to the ground in exhaustion. She struggled to climb to her feet, but her muscles screamed in rebellion, and she sank back down.

In her head, she begged for one of the Metroids to come to save her, but she knew it was helpless. She had to face the X-Brain alone.

The terrible fusion of flesh and metal stepped toward her now, evidently savoring the moment. The energy began to gather in its eye again, and Samus knew that she would not survive the next attack.

As the X-Brain fired once more, Samus flattened herself to the ground – and, miraculously, the beam passed harmlessly above her head. The X-Brain, seeing this, attempted to lower the beam, but it was slow-moving, and Samus rolled out of the way.

Feeling strength returning to her, now, Samus managed to get up on her feet, panting with the difficulty of the effort. Her ears were ringing, her eyes blurred, her breath heavy…but she had survived.

With strength she didn't know she had, Samus somehow managed to leap up onto the X-Brain's head, dematerialize the glove covering her left hand, and plunge the Metroid-like claw into the monstrosity's fleshy form.

It screeched in protest, waving its head to and fro in a desperate attempt to shake Samus off, but the bounty huntress held on for dear life, refusing to let go. Slowly, its movements stopped, and it collapsed to the ground as Samus had earlier, devoid of energy. The body dissipated, and the brain simply fell apart. Then, something burst out of it.

A Core-X.

"I've just about had it with you guys," Samus snarled, reinvigorated with the energy obtained from the X-Brain. Placing her palm and arm cannon alongside each other, she fired the most powerful shot she could muster from each, disintegrating the Core-X's membrane and leaving behind only the helpless X within. Samus leapt up and absorbed it into her body.

Unintelligible script suddenly appeared on her visor from the absorbed Core-X. Samus frowned.

"Adam, can you translate this?" she asked. There was a pause, then a response. "No. I've never seen that language before."

Samus sighed. "Well, I guess this ability – whatever it is – is useless to me, then." She disabled it, and the script disappeared.

She glanced around, expecting a siren to start sounding. Every time she had defeated the Mother Brain in the past (and even when she had defeated the extremely similar Aurora Unit back on Phaaze), the planet, or at least the area, had become unstable and exploded. There was no sign of anything like that happening now, though.

"That's odd," Samus murmured. "I'd been counting on an explosion…it's what I'd hoped to use to rid this planet of the X…"

"They probably disconnected the Mother Brain from the main planetary control to prevent something like this from happening," Adam reasoned. "Better that the person who killed the X-Brain remain alive than the rest of them die."

Samus sighed. "You're right. Well, maybe this time, at least, Mother Brain will _stay dead_ for once."

"We should probably return to the surface," Adam suggested.

-=-=-

As Samus reached the exit of the caves, a shot rang out from somewhere nearby. Moments later, a bullet whizzed right by her helmet.

"Hello, Aran!" somebody cackled from nearby. "I've been waiting for you here!"

A man was sitting atop a rock, his gun in his lap. His face was obscured by the sun.

"Who are you?" Samus called up to him. "What do you want?"

The man leapt down from the rock, and Samus gasped in spite of herself as she saw his face. Half of it was disfigured beyond belief, his skin turned a translucent green and his skull visible beneath. He wore a tattered Federation uniform. His eyes were a bloody red color, and his hands turned to green…Metroid-like claws…

Samus lifted her own hand for comparison, and her eyes widened as she saw that they were identical.

"Who are you?" Samus repeated.

"You don't know who I am?" the man laughed, his eyes glinting in the sun. "You should. You really should. Everyone knows who I am."

"Enough with these games," Samus snapped. "Just tell me who you are already."

The man sighed. "Fine, fine. After all, who am I to deny the _great Samus Aran?_" he asked mockingly.

"I'm Galactic Federation President Martin Rodriguez."

Samus stared at the man, dumbfounded. "You're joking," she said slowly. "You've got to be joking."

"It's no lie," Rodriguez said cheerfully. "I may look different from what you've seen on the television, but I'm still the same man on the inside."

He laughed again.

Samus slowly raised her arm cannon. "What do you want, then?" she asked testily.

"Oh, nothing much…" Rodriguez chuckled. "Just your head for display in the Federation capital."

With that, he snapped his fingers, and the hideous experiments from the Valhalla emerged, snarling and growling at Samus.

"Go and fight them," Rodriguez said giddily. "This is what you wanted, isn't it? To bring an end to my experiments? Well, here's your chance! Kill them! Kill them all now!"

Samus lifted her arm cannon and aimed at them hesitantly, then lowered it, even as the creatures approached. "I won't fight them."

Rodriguez gaped at her. "What? What? Why not! Look at them! They're products of those immoral experiments of mine you hated so much! Kill them and end it here and now!"

"I won't fight them," Samus repeated.

"They're freaks! They don't belong anywhere! The universe would be better off without them! They would be better off without the universe! You kill them and everybody wins!"

"They didn't choose to be the products of your experiments," Samus replied coldly. "They don't deserve to be punished for something that wasn't their decision."

"They're freaks!" shouted Rodriguez, delusional now. "Mutants! Abominations! Monsters! Freaks! They're freaks just like you and I are!"

"Are you saying," Samus said slowly, "that we should die too?"

"Of course!" Rodriguez cackled. "Look at me, look at you! Two mutant peas in a pod! Kill all of them, then kill ourselves! Great idea, isn't it?"

Samus shook her head. "You're insane. I won't kill anything here."

Rodriguez began to tremble with rage. Suddenly, he whipped around, and, lifting his gun, he shot each of the experiments, their mangled cries echoing across the environment. When he was done, a pool of blood bathed the area.

"There," Rodriguez growled. "I did it. Because you're too pathetic to do it."

Samus stared at the fallen carcasses of the experiments, an unfamiliar feeling in her chest.

"Now there's just one more freak to kill…" Rodriguez continued.

Samus looked back at him. "You're insane," she repeated. In response, the Federation president raised his gun and fired at her. Samus twisted out of the way, and the bullet passed by harmlessly. She leapt up onto the rock Rodriguez had been sitting on earlier.

"You can't run, Aran!" Rodriguez cackled. "The only way to end this is for one of us to kill the other!"

"I won't kill anything here today," Samus repeated.

"Then we can wait until tomorrow!" Rodriguez laughed.

Samus sighed and closed her eyes. "No," she said. "We won't wait for anything."

She flung out her hand, and her grapple beam attached itself to Rodriguez. She flung him upwards, and he dropped his gun with the force. He landed on the rock next to Samus, and she placed her arm cannon to his head.

"I said I wouldn't kill anything here," Samus said. "But as far as I'm concerned…you lost your status as a living being a long time ago. You're nothing. So I won't be breaking my word when I kill you."

She fired, and the president's eyes rolled up into his head.


	11. Part 11

**FINALE - PART 2**

Samus sat there with the president's carcass for a few minutes before it occurred to her that he must have landed a ship around there somewhere. She stood up, slung the corpse across her shoulder, and set off.

"What are you doing?" asked Adam.

"Looking for his ship," Samus grunted in reply. "We need to get off this planet somehow, and why not travel first-class?"

"I mean with the body," the computer elaborated. Samus paused for a moment.

"We should probably give it back to the Federation at some point," she said. "They can decide what to do with it. It's not in my authority to determine the fate of a Galactic Federation president's body."

"Since when have you ever cared about authority?" Adam asked dryly.

"Point taken," Samus replied. "Still, though. We should let them see what happened to him."

The president's private cruiser came into view, a sleek, spacious ship. Samus peered in the window and walked away impressed. The seats even had cupholders…!

She found the door, and the darker side of the ship became apparent. The remains of shattered stasis tubes lined the walls, and Samus realized, with an unpleasant lurch of her stomach, what they had held before they had been broken. She set the body down in the corner, where she wouldn't have to look at it, and hastened to the pilot's seat. She promptly lifted off.

Samus found the communications unit, and called Ashen Feather. The Chozo picked up at the first ring.

"Samus? Is that you?"

"It's me," confirmed the bounty huntress. "Where are you right now?"

Ashen Feather gave her their coordinates. "Do you have a ship?" he asked her.

"Yeah," Samus said. "I'll explain everything once I get there. Any news on the Space Pirates?"

"Plenty," Ashen Feather replied grimly, "and none of it good. We'll explain once you get here, as well."

-=-=-

As Samus landed on the outpost, the whole group was there to meet her: Ashen Feather, White Voice, Tarus Wesley, Odius, and the rebel Space Pirates. Not one of them looked cheerful.

Samus stepped out of the hatch. "Well…here I am," she said hesitantly, noticing their somber expressions.

"Come inside," Odius said. "We've got a lot to talk about." He led them all through a door, into a dingy room lit only by a small lamp above a table.

"First things first," Odius said once they were all seated. "Samus, what have you accomplished?"

Samus recounted her experiences on Zebes, neglecting to go into detail about the president's madness. She decided that they didn't need to know that much about it…besides, she didn't want them to start worrying about her again…

"That strange script you mentioned," Ashen Feather began slowly. "Could it have been Chozo script?"

"Couldn't have been that," Adam replied. "My translation files include Chozo script, and it didn't match any of them."

"Regardless," Ashen Feather rebutted, "you should at least let me take a look at it to see if I can help you out."

"We can worry about that later," snapped Odius. "Right now, we've got a bigger problem on our hands."

"What's wrong?" Samus asked.

The pirate leader sighed. "Where to begin, where to begin…first of all, a group of Space Pirates have detached from the main forces and have rallied under the rule of Ridley. Now they're engaged in a civil war with each other…"

Samus frowned. "I don't get it. Isn't that a good thing for us?"

Odius shook his head. "When they were all united, we only had one faction to win over to our cause. Now, with two warring sides, it'll be that much more difficult."

"I see," the bounty huntress said, nodding. "Continue."

"Second, the main sect of High Command – Auros, Ferrix, and Duma, for those of you who don't know – has formed an alliance with the Federation…although I don't know what'll become of that thanks to the death of the president. And finally…remember those X Parasites the Federation deployed on Tallon IV? Turns out they're Metroid-resistant. Ridley found out about this and took some of them to use in the war."

"Metroid-resistant?" repeated Samus. "So…are you saying that even I could be infected by one of these things…?"

"That's exactly what I'm saying," said Odius grimly.

Samus sighed. "Well, we've come too far to let something like this stop us. Metroid-resistant X or no, the Space Pirate Empire must come to an end."

"Don't be so headstrong, Samus," Ashen Feather warned. "Let's think rationally. We can wait it out."

Samus shook her head. "No, we can't. You know how fast the X multiply, don't you? If we wait, this new form of them will overrun…wherever this war is taking place. Better to attack now, when there aren't too many of them."

"I agree with Samus," Wesley said quietly from a corner. Samus turned around to rebuke him for his cowardice before she realized what he had said.

"Fine," Ashen Feather said grudgingly. "We'll attack now. But we need an actual course of action."

"That, we can make," Odius replied, satisfied. He laid out a map on the table. "Here, we have a map of the main pirate stronghold on Earth."

"Wait a minute," Samus said. "Earth? As in, the home planet of the human race? That Earth?"

Odius nodded. "The very same."

"When did this happen?" Samus asked with wonder.

"Once humanity had evacuated the planet after they had polluted it beyond belief, the Space Pirates came across it. While its conditions may have been inhabitable to your people, it was quite hospitable to us. Since the Federation would have no reasons to revisit it, the Pirate Empire set up a base there. Eventually, it became the seat of High Command."

Samus blinked. "That…all this time, we had the pirate stronghold right in front of our eyes, and we didn't even notice…"

"Anyway," Odius continued, "Ridley is currently laying siege to the various forts out there, slowly moving closer to High Command's main base. There's no doubt in my mind that he'll make it there; Ridley's a military genius. So, we follow behind him, keeping out of sight, letting him do all the hard work for us. Then, once we reach the main base, we find the room where backups of all the minds of the members of High Command are stored. We destroy them, then find a way to kill High Command itself. Sound good to you?"

"No complaints here," Samus said, satisfied. "Let's get going."

-=-=-

Tarus Wesley stared out the window of the ship, watching the stars go by. Soon, all of this would be over. Soon, he could go back to his normal life.

He was aware of Samus walking in his direction. She came to a stop beside him.

"You confuse me," she said, and Wesley turned to look at her. The eyes behind the visor seemed to be boring into him.

"How so?" Wesley asked.

"Back on the Valhalla, you showed yourself to be a complete coward. You were unreasonably afraid of the prospect of death. You're different now. I'm not going to ask you what caused you to change, but I do wonder this: why become a soldier if you're so frightened of the thought of death?"

Wesley sighed.

"My sister was the victim of a Space Pirate raid," he said. "They caught both of us and killed her first. They tore each of her limbs off…I was forced to watch. I was going to be next, but I was saved by a Federation trooper."

"Do you know who led the raid?" Samus asked.

Wesley shuffled uncomfortably. "Ridley. Who else?"

Samus nodded distantly, staring out the window at the stars as Wesley had been earlier.

"Anyway," he continued, "I joined the Federation military to avenge my sister…but at the same time, I'm afraid to share her fate. It doesn't make much sense, I know…"

Samus shook her head. "No, it makes perfect sense."

She continued staring out the window for a minute before she spoke again. "I watched my mother die," she said softly.

Wesley glanced over at her.

"I was a child…I tried to make peace with Ridley, fool that I was, and he was about to kill me with a fireball. Then, my mother…she jumped into the way to protect me…"

Within the visor, Wesley could've sworn he saw a tear running down her face.

"And my father…he killed himself, trying to take down the pirate forces with him…"

She turned to Wesley. "The deaths of the people we love…that's what shapes who we are, isn't it? You watched your sister die, so you tried to avenge her death, but feared the same thing happening to you. My mother died trying to protect me, my father trying to destroy the pirate forces, so I fight to protect others and to destroy the pirate forces even if I die in the attempt."

"I guess…you have a point," Wesley said uncertainly.

Samus nodded. "Thanks for this conversation. I feel a lot better, now." She walked off.

Wesley watched her go, and the wheels began turning in his head. _She expects to die,_ he realized with shock.

* * *

"There," Odius said, pressing his finger to the window. "There it is."

The once-blue surface of Earth stretched out before them, now a mottled brown. Turbulent clouds swirled around its six continents (the seventh had melted long ago).

"That's Earth," Samus muttered to Wesley, a sarcastic smirk on her face. "That's where we came from. We crawled out of that pit."

"It wasn't always that bad, though…" Wesley pointed out. "They say that it used to be beautiful."

Samus didn't respond.

"The High Command main base is on that continent," Odius informed them, pointing to Africa. "It's on the southern tip, so we should probably land somewhere around there." He glanced around. "Any objections?"

"Will we have to wear helmets?" asked Ashen Feather.

"No, the air on the planet's breathable. You shouldn't be in any real trouble unless you stay there for more than a week."

"Let's go, then," Samus said. "We've waited long enough."

Nodding his agreement, White Voice took the controls and began to take them down to the planet.

-=-=-

A bleak and barren landscape greeted their eyes as they set down, devoid of any sort of life. In the distant horizon, they could see small lights dancing across the sky – explosions from the battling Space Pirates. Samus was the first to set foot on the hard, cracked earth, followed by Odius, Wesley, White Voice, Ashen Feather, and Odius' troops. They set off without delay.

The first few hours of their hike were uneventful. No conversation passed between them; there was nothing to talk about. From time to time, they would think that they'd heard a noise, but it would turn out to be nothing.

Then, they came across the first battleground.

Corpses and innards were strewn across the field, a gory spectacle. Aside from them, nothing moved in this graveyard; Ridley's pirates had left no enemy alive.

"Over here," Odius called, pointing at the ground. Samus was the nearest, and came over to him at a jog. She inspected the distinctive footprint he was pointing to.

"Ridley," she growled simply, and continued onward.

As they walked, they came across more and more of these battlefields, often accompanied by the smoking ruins of a fort. Once, they accompanied a living pirate whose eyes had been gouged out and his legs broken. They put him out of his misery.

The lights in the sky were becoming more distinct, and they knew that they were getting closer to the fighting. Once, a large pirate carrier passed overhead, flying in the same direction they were heading.

Then, after eight hours of walking, the army came into view.

It was considerably smaller than they had been expecting; maybe around five hundred troops. A familiar draconic shape flew around above the army, and their small group could just barely hear his voice as he barked out orders.

"We should probably wait," Ashen Feather reasoned. "We don't want to get too close."

The others agreed, especially since the sun was beginning to go down. One of the burned-out forts was nearby, and they resolved to spend the night in it.

-=-=-

Wesley's eyes shot open and he sat up as the first quake hit. What was that…?

Another one, closer now. "Samus," he hissed, trying to awaken the bounty huntress. "There's -"

"Quiet," Samus snapped. She was already awake and looking around, trying to find the source of the quakes. "Wake everybody else up, but don't make any more noise."

Wesley nodded silently, and proceeded to shake them awake, placing a finger to his lips as he did so. Samus seemed tenser than usual, and he didn't want to risk her ire.

When the third quake hit, practically directly under them now, Samus seemed to make up her mind. "We have to leave. Now," she ordered, eyes scrupulously scanning their surroundings.

They had barely begun to move when the fourth quake hit, and the ground crumbled beneath them. Most fell into the yawning maw of the darkness, shouting for help. Samus, miraculously, was near the wall, and managed to kick off it back to the surface, where she found Wesley dangling there by his arm. She helped him up, and the two fell to their knees, panting with exhilaration.

"What happened?" asked Wesley, frightened. "What were those quakes?"

"They saw us," Samus said grimly. "I don't know if it was from that ship or if it was just that we were too close, but they saw us." She seemed angry with herself. "They tunneled their way below us and detonated bombs to weaken the earth, then trap us."

"Do they know that you're here?"

Samus shrugged. "Who knows? They'll probably realize that they didn't get all of us, but as to whether or not they'll connect them to me, well…"

She glanced at the frightened Wesley. "You can go back, if you want," she offered.

Wesley shook his head. "No, I'm staying."

"Glad to hear it," Samus said. "Now let's get going."

She began to walk, but Wesley stood there, squinting at the horizon.

"What's wrong?"  
"Is…that our ship...?"

Samus followed Wesley's gaze to the approaching vehicle. There was another pirate carrier…and attached to it, strapped to its hull, was the president's private ship that they had used to travel to Earth.

"One moment," Samus said, and aimed her arm cannon at the carrier. When it was close enough, she fired three Super Missiles at it. Each hit in a different spot, and the carrier crashed to the ground, releasing their ship in the process. A Space Pirate flew out of the pilot's seat and was still.

Samus jogged over to their ship and forced the door open. Everything within it was intact, including Samus' old Power Suit and Rodriguez's body. When she went over to the controls, though, she found none of them working.

"Do you have any experience in ship repair?" Samus asked as Wesley walked up to her. He responded that he didn't. Samus sighed and sat down. "Well, can't have everything, I guess."

"I can provide you two with instructions," Adam offered.

"Sounds great," Wesley agreed, and they got to work.

-=-=-

Odius landed hard on his back, and he was immediately hauled to his feet by two pirates. "Well, isn't this an odd group…" murmured their leader, stepping forward. "A squad of Space Pirates and two Chozo? Strange. Very strange. Why have you detached from the rest of Ridley's forces, hm?"

"We're not a part of Ridley's forces," Odius snapped. The other pirate raised an eyebrow. "Oh? Then are you on our side? We never authorized any unit to detach from the main force."

"Perhaps I outrank you," spat Odius. The other laughed at this, bemused. "Do you know who I am?" he asked, stepping closer.

Odius studied the other's face before his eyes widened. "You're a part of High Command," he gasped.

"Precisely," he said, satisfied now. "Ferrix, to be exact. Now…please answer truthfully. What were you doing here?"

Odius sighed. "…Trying to rid the Pirate Empire of High Command," he confessed.

Ferrix smiled mysteriously. "Does that include Ridley?"

Odius nodded. "It does."

Ferrix continued to smile, and paced around them, paying particular attention to Ashen Feather and White Voice. "It's been quite some time since I've had the opportunity to meet a Chozo," he commented. Ashen Feather stiffened. "I can't imagine why," he muttered sarcastically.

Ferrix paused. "Samus Aran was traveling with you, wasn't she?" he asked in a low voice.

"No," Ashen Feather lied. Ferrix sighed. "I had hoped that a Chozo would be above lying," he said sadly. He turned to White Voice. "What about you? Will you lie to me as well?"

White Voice merely stared at Ferrix, his expression unreadable.

"He's mute," Ashen Feather explained. "You won't get any responses out of him."

Ferrix scowled and turned back to Odius. "You're the leader of these troops, correct?" he asked, gesturing to Odius' pirates. He nodded. "That's correct."

Ferrix signaled, and his soldiers opened fire on Odius'. They dropped to the ground, dead. Odius was startled.

"That's the punishment for lying," snarled Ferrix. "So I ask you once more: was Samus Aran traveling with you or not?"

Odius bowed his head. "She was," he mumbled. Ferrix's smile returned. "Much better."

He turned around, heading back into the tunnel from which they had come. The others hastened to follow him, holding Odius, White Voice, and Ashen Feather in their custody.

"You said your goal was the downfall of High Command?" said the pirate holding a gun to Odius' head.

"Yes, exactly," Odius replied coldly. "I'm sick of their rule."

The pirate nodded thoughtfully. Then, he took the gun off Odius' head…and fired it at Ferrix's exposed back.

The High Commander fell to the ground, and the pirate took the opportunity to fire several more shots at him. In an instant, pandemonium broke loose as the confused pirates tried to figure out what was going on. "This tunnel leads directly to the High Command building," hissed the pirate who had shot at Ferrix in Odius' ear. "Auros and Duma are in there, and Ridley should arrive before long. I may as well have forfeited my life for this cause…you'd better succeed." With that, he pushed Odius forward even as the other pirates began firing at him.

White Voice and Ashen Feather had managed to escape as well, and together they raced through the tunnels, praying that their pursuers wouldn't catch up with them.

-=-=-

"That should do it," Samus said. She walked over to the controls and tried them again. They now worked perfectly.

"…Samus," Wesley said quietly. The bounty huntress glanced over to her companion.

"You're planning to fight Ridley, aren't you?" he asked.

Samus hesitated before nodding. "Yes. I am."

"You know that he'll probably have those Metroid-resistant X with him, right? Not to mention the rest of his army?"

"I'm well-aware of that. What are you saying?"

Wesley frowned. "That's suicide, Samus."

"What else can we do?" she asked, shrugging. "This is our only chance. He's not going to get any weaker…and if you're afraid, you can still leave at any time."

Wesley shook his head. "I'm not afraid," he insisted. "There's a difference between being afraid and being reasonable. You just don't have a chance. Look…I understand that you're the most powerful woman in the galaxy. But not even you could survive against those odds."

"What else can we do?" Samus repeated.

Wesley closed his eyes and took a deep breath. "Look…if you're dead-set on doing this, then at least rest up a bit. You need all the strength you can get for this."

Samus sighed. "Fine. If you insist…I guess you have a point."

Wesley looked relieved.

-=-=-

The stone of the tunnels gave way to metal, and Odius, White Voice, and Ashen Feather realized that they were now within the High Command building. Within moments, they turned a corner and discovered an elevator, with stairs beside it.

"Take the stairs," Odius ordered. "The elevator's too risky."

Nodding, they ascended the stairs and emerged into a grand lobby, suspiciously empty of any pirates. The floor was made of a peculiar variety of stone, while the ceiling was translucent. Two more staircases went in opposite directions on either side of the room. Every few moments, there was a distant boom; they realized that Ridley's forces had reached the High Command building and were laying siege to it right then and there.

"We can't stop," Ashen Feather said. "Just choose a direction and let's go."

Odius nodded and chose the staircase nearest to them. As they hurried up the steps, the shadow of a great, winged beast passed above them, and they all glanced at one another anxiously. Ridley had arrived.

Moments later, they heard a great crash, and they knew that Ridley had broken into the building. They hesitated. The crash had come from the direction they were going in, and there was only one door at the top of this staircase. Could they risk going through it…?

Their questions were answered immediately as they heard another crash, and saw Ridley flying overhead again. Not wishing to press their luck, they raced up the remaining stairs and entered the door. Behind them, they heard yet another crash; Ridley had entered the lobby from the ceiling.

This room, too, was devoid of troops; only weapons and armor could be found here. Ashen Feather and White Voice took this chance to arm themselves, taking guns with bayonettes attached to them. Odius, too, replaced his weapon with a more efficient one. Once they were done reequipping themselves, they went through the next door. There they found a large rotating machine in the center of the room, situated above a transparent surface. Looking down, they saw a giant hole with no visible bottom; every few seconds, the machine would send down a charge of energy. Its purpose was a mystery to them.

The next room was enormous; it was filled with hundreds of strange, red-colored pods. There was one larger pod in the center of the room, connected to the rest. Odius broke open one of the pods, and the grotesque visage of a half-formed Space Pirate greeted him.

"These are the cloning vats," he realized. "This is how the Space Pirate army is populated…I was probably born in one of these. And that means…"

He went over to the central pod and opened it. The ideal Space Pirate floated unconsciously within it; strong, agile, and obedient. He tore the pirate out of the pod and fired at it, killing it instantly.

"There," Odius said, satisfied. "That's what I think of these cloning operations."

The next room was the first one that Ridley had entered. The roof now covered the floor, exposing the room to the open air. There were four of the cloning vats in this room. Three of them had been broken, and Odius had an odd suspicion that he knew what was in the fourth.

"Unfortunate, isn't it?" asked a voice from behind them. They leapt up and turned around to meet the face of another of the High Commanders.

"He has destroyed our replacement bodies, and now he targets our replacement minds. Once he is done with that, he will kill us, and then High Command will be no more."

"Are you Auros or Duma?" demanded Odius

"…Why do you neglect Ferrix?" the High Commander asked, confused.

"He's dead already," Ashen Feather replied curtly. "Killed by a pirate sick of High Command."

"I see," said the pirate leader gravely, closing his eyes. "I am Duma. Tell me…is it my fate to die today, as well?"

"It is," confirmed Odius.

Duma sighed, his eyes opening. "Very well. I accept my fate without struggle. Ferrix may have deluded himself into believing that he would survive this day, and Auros may attempt to defy fate, but I realize that there is no point in this. Besides…I am tired." He gave them a weary smile.

"But at the very least…oblige this old Space Pirate and allow me to see the destruction of what is stored in that pod."

Odius nodded. "Fair enough." He pried the pod open, and there, curled up within the cloning vat, was the sleeping form of a young space dragon – a child-Ridley. Even as a child and asleep, he still looked vicious. Without hesitation, Odius took White Voice's bayonette and slashed its throat.

Duma nodded his satisfaction. "Very good. We are one step closer to the death of Ridley. Now…do with me what you will."

Odius sighed. "I regret having to do this…you don't seem nearly as corrupt as the others."

Duma shook his head. "No. My deeds were just as atrocious. I deserve my punishment."

"So be it."

Odius circled around behind Duma, and shot him at the base of the brain, making his death as quick and painless as possible.

He glanced up at White Voice and Ashen Feather. "One more," he said simply.

-=-=-

Ridley and fifty troops now occupied the lobby of the High Command building. The rest of the troops had been ordered to go ahead to the shore, in order to pick off any stragglers who thought they would be able to escape.

He was waiting in this lobby for exactly one reason: he had been alerted that none other than the Hunter herself, Samus Aran, was on her way here. She had been witnessed walking in this direction earlier, and her goal was quite obvious.

Fine, then. She wanted a battle…he would give her the battle of her life.

He was patient. He could wait to kill High Command. Cowards that they were, they would never dare to attack him. Besides…as much as he hated them, he hated Aran that much more.

Ridley grinned slightly, imagining crushing the Hunter, smashing her into tiny bits, unleashing all his fury on her. There was no doubt in his mind that this would be the day; this would be the day that he would kill her once and for all. Aran was good…but she was not nearly good enough to handle fifty troops all at once. Oh, sure, she might manage to defeat them…but by then, she would be easy picking for the space dragon.

There it was; the familiar ring of the Hunter's arm cannon. She wanted them to know that she was here.

And then, moments later, she entered. Ridley noted her new blue and white suit, but wasn't in the least bit surprised; he was well aware by now that she often obtained new Power Suits.

Aran appraised Ridley and the pirate forces coolly, her eyes wandering across each of them. Ridley took this opportunity to speak.

"Samus Aran," he sneered. "So you've finally come. Do you think yourself capable of handling all of us?"

She didn't respond, but continued to stare at Ridley. The space dragon found her silence somewhat unnerving, but decided to disregard it.

"ATTACK!" he screamed, and all hell broke loose.

Aran briefly charged a missile, then fired it off at the nearest pirate. As it struck, a wide explosion issued forth from it, diffusing across the whole room and knocking each of the pirates back. None of them were killed by the attack, though, and they then began their attack in earnest, pressing in against the Hunter, forcing her to fight for her life. At that point, she was forced to fire off uncharged shots and missiles; she didn't have enough time to charge them up.

Ridley saw where this battle was going, though. He was expecting it, and eagerly anticipating it. His predictions were confirmed when he saw the first pirate fall.

The first pirate to die was hit by a Super Missile. It was knocked back into its comrades, briefly incapacitating them and giving Aran some slight breathing room. She used the opportunity to charge her beam, and fired it off at the horde, killing three more. The attacks resumed promptly, but the tides were slowly changing in Aran's favor.

Ridley continued to watch the battle from afar, but the Hunter had other plans. In the midst of her attacks, she aimed her arm cannon at Ridley and sent a Super Missile his way. Surprised, the space dragon only barely managed to fly out of the way. In anger, he spat a fireball at Aran, which, thanks to her limited moving room, was a direct hit. She seemed somewhat satisfied, though…

Was she trying to involve him in the fight?

As the battle went on, Aran continued to send an attack Ridley's way at every opportunity, forcing the space dragon to keep on his toes. Some of the attacks managed to connect successfully, a lapse in his reflexes. He was infuriated by these, but resolved not to involve himself in the fight; not until the rest of the soldiers were killed, anyway.

She was down to thirty, now; the room was strewn with dead pirates. While Aran had, at first, been forced to take the defensive, she was now going all out on the offensive; the pirates continued their onslaught, but it wasn't enough. It was whittling her down, but they would be dead before she was.

And when the last shot hit, and the last pirate fell to the ground dead, the Hunter was victorious.

She turned to Ridley, fire blazing in her eyes. He clapped mockingly. "Very good," he jeered. "But I would expect no less from the Hunter."

Still no response from her.

"But now it's my turn," he said, resolving to continue the conversation on his own.

With that, he screeched and flew in her direction, mouth ablaze. Before she could get out of the way, he grabbed her in one claw and slammed her against the wall before unleashing the most ferocious wave of fire he could muster. He expected to hear her scream with pain, but there was still no sound from the Hunter. Ridley was confused. Why was she so unusually silent…?

When at least the stream of fire ended, Aran hung limp there, her armor scorched, her visor stained with soot. She attempted to lift her arm cannon, but even that task seemed beyond her strength.

"I was hoping for this, you know," Ridley hissed, trying to get a response out of her. "You would spend all your energy on fighting my troops, then I could end you myself. You fell right into my trap, Aran! You…"

Just then, he noticed something odd. Her eyes…

Those were not her eyes.

He grabbed the helmet and pulled it off. "You're not Aran," Ridley murmured in shock.

"Surprise," Tarus Wesley spat, lifting the arm cannon and giving Ridley a Super Missile to the face.


	12. Part 12

**FINALE - PART 3**

"…p! Damn it, Samus, WAKE UP!"

Samus' eyes shot open, and immediately she realized that something was wrong. Her Power Suit was gone.

"What happened?" she demanded. Adam, who was now on the shipboard computer rather than in her helmet, responded. "Wesley happened. He stole your Power Suit, put me in here, and went off to fight Ridley."

"Is he insane?" Samus wondered. "If he thinks that I won't be able to handle Ridley along with all his soldiers, what makes him think…"

"That's just it, Samus," Adam said grimly. "He knows he can't beat Ridley. He intends to even the playing field for you…"

"…He told you this?"

Samus took Adam's silence to mean a "yes."

She closed her eyes. "How long of a walk is it from here to the High Command building?"

"Two hours," Adam replied.

"And how long has it been since Wesley left?"  
"…Three hours."

"…I see."

She walked over to the cargo hold, where her old Power Suit was sitting. She suited herself up, beginning with her helmet and continuing down. At last, she was ready.

"Let's go," Samus said. "We won't let Wesley's sacrifice be in vain."

-=-=-

Odius, Ashen Feather, and White Voice reentered the main cloning chamber, all of their senses focused on finding the final member of High Command. Auros was the only one remaining; they were so close, now. If they could find him…

They hurried into the room with the mysterious spinning machine, and, miraculously, there he was; the final High Commander, their final battle, the only thing standing in the way of their victory. But…

Auros turned around, and they saw it; the blank, emotionless eyes, the faint discoloration, the way he moved…he had fallen victim to the X.

It stared at them, as if waiting for them to make the first move.

"What do we do?" asked Odius, hesitant to fight an X Parasite.

"Maybe we should just try to escape…" Ashen Feather said doubtfully. "We can wait for Samus…maybe she's come up with a way to defeat the Metroid-resistant X."

They started moving in the direction of the next door, but White Voice remained still.

"Come on," urged Odius. "It's not attacking us. We can still escape…"

White Voice shook his head.

"You're…going to try to fight it…?"

He nodded in response.

"We'll stay and fight too, then."

Another shake of his head. Ashen Feather was about to protest when White Voice held out his hand, and an unseen force pushed them through the door. It locked as soon as they were through, and White Voice turned back to the X-infected High Commander.

They locked eyes, and leapt into action.

Slimy tentacles burst out of Auros' back, a product of the X's ability to mix and match the assets of the hosts it had infected. One of the tentacles grabbed White Voice around the midsection and threw him against the wall, bits and pieces of it crumbling off with the force of the impact. White Voice's hands began to glow blue, and suddenly the tentacle unraveled before being yanked in the mute Chozo's direction.

Watching through a window in the door, Ashen Feather's eyes widened. "I don't believe it," he whispered. "He's mastered the magic of the Chozo…"

"Magic?" repeated Odius, understandably skeptical.

"Well, it's not really magic…but it's an ability that most Chozo have but aren't able to harness."

They went back to watching the fight with rapt attention.

A blade now shot out of Auros-X's wrist, and the infected pirate raced toward White Voice. The mute Chozo, in response, raised the bayonette of the gun he had taken. The two exchanged a few blows before the bayonette was knocked out of White Voice's hands. Auros-X now swung its blade at the undefended Chozo, but White Voice simply disappeared before reappearing atop the rotating machine a moment later. His hands glowed blue once more, and suddenly the blue glow extended from his hands to form the shape of a sword.

Auros-X leapt up on top of the machine, and the two continued to parry one another's slashes, each attempting to deal a fatal blow to the other. The infected pirate suddenly lashed out with one of its tentacles, wrapping it around the other's sword arm. It used this opportunity to slash White Voice's throat.

Ashen Feather gasped, believing it to be over…but White Voice ran his free hand across the wound, leaving behind the familiar blue glow. The blood seemed to be frozen in place.

Then, he pushed out with his hand, and Auros-X flew back, landing at the edge of the machine. White Voice regained his composure, and the blue glow around his hands pulsed slightly, becoming white before turning to a slightly duller shade of blue.

"He can't keep this up," Ashen Feather murmured. "This type of magic uses up his life force. If he uses too much of it, then…"

He didn't have to finish his sentence to explain to Odius what the result would be.

Auros-X scrambled to its feet, lunging at White Voice once more. The Chozo was prepared, though. The blue surrounding his hands intensified, and as the pirate came within reach, he plunged one of his hands right into the High Commander's chest.

There was no gore, though, and the infected pirate didn't seem to be in pain; its eyes were wide, but out of shock more than anything else.

When White Voice removed his hands from the pirate's chest, he was holding an X Parasite.

Auros stumbled backwards and fell to the ground, bewildered but still alive.

White Voice glared at the writhing mass in his hands, and the blue turned to white again. He was focused on pouring this energy into the X, trying to kill it. The X, in turn, stretched, reaching out in White Voice's direction, trying to infect him.

But the white light began to fade, turning to a bright blue, then dulling more and more until it was black. White Voice's eyes were half-closed at that point, and the X escaped from his grasp and entered his body.

Then, the white light returned, surrounding the Chozo's entire body now. Somehow overcoming his mute condition, he let out a bloodcurdling scream. The floor beneath him shattered, and as he took his own life, he fell into the abyss.

The door somehow unlocked itself, and Odius and Ashen Feather burst through.

"He did it," Ashen Feather murmured with wonder. "He…he removed an X from someone while keeping them alive…"

"He kept me alive," Auros whimpered, somehow knowing their purpose there. "Won't you honor his decision?"

Ashen Feather shook his head. "No…we came here with the intention of ridding the universe of High Command. Besides…your life is already over. Nothing can undo what's been done here today."

Even as the High Commander groveled at his feet, begging for mercy, Ashen Feather fired at him, finishing the job that White Voice had not. Auros fell to the ground, moving no longer.

"…And that's that…" murmured Odius. "We've done all that we came here to do. All we can do now is wait for Samus to arrive and take care of Ridley…"

-=-=-

As Samus entered the lobby, she didn't fail to notice the numerous Space Pirate bodies spread all across the ground. She felt a twinge of both pride and pain, proud of what Wesley had done…yet knowing all too well what the cost of that had been.

Ridley was facing the wall, but turned around as he heard Samus approach.

"There you are," he growled. "Care to confirm to me that you are who I think you are?"

Samus removed her helmet, letting Ridley know without a shadow of a doubt that it was the real Samus Aran he was facing, then put it back on.

"Where is he?" she demanded. "What did you do with him?"

Ridley gestured off to one side, where Wesley's broken body was propped up against the wall. He was still in the Protector's Suit. Samus walked over to him, praying for the impossible yet knowing what she would find. She checked his pulse, and her suspicions were confirmed.

"You didn't plan this, did you?" Ridley asked coldly, his eyes on Samus. "No…you didn't. I can tell. He did this of his own accord."

Samus stood up, shaking with both despair and rage.

"He cheated me of my victory," Ridley continued. "You would have come here and fought all my troops, and triumphed. But then you would be worn out, and I would kill you. But instead, all those troops were wasted on this worthless little pest."

Samus turned around. "You are," she snarled, "the most disgusting rat in the universe."

Ridley smirked, taking this opportunity to toy with Samus. "What, still angry about Mommy?"

"SHUT UP!" she roared, launching a Super Missile Ridley's way. Predicting this, the space dragon easily stepped aside.

"And what about poor old Daddy? The old fool thought he could end us by blowing himself up…you know, one of my surviving soldiers managed to hear his last words. Would you like to hear them?"

Another Super Missile was Samus' response, but Ridley once again dodged with ease.

"Well, here they are: 'Samus, I love you!' Isn't that just adorable?" he asked mockingly, laughing.

While he had been busy taunting Samus, though, the bounty huntress had rushed up to him. An arm cannon to the face was enough to shut him up.

"Fine, then," he hissed. "Enough play."

He whipped his tail around, slamming it into Samus and knocking her away from him. Then, he went up into the air, flames licking at his teeth. Samus followed him with her arm cannon, waiting for the right moment to fire.

Then, Ridley made a u-turn and swooped downwards, flying directly at Samus now. Even as she began to fire her missiles, he let loose four large fireballs. Ridley dodged two of the Super Missiles, but the others were homing, and three more impacted on his skin, leaving burn marks there. Samus, meanwhile, leapt out of the way of the fireballs, but was singed on her right side.

Ridley, not pausing for even an instant, flew at Samus and attempted to snatch her up with his claw. The bounty huntress turned to her morph ball form, rolling out of the way and leaving the space dragon grabbing at empty air. He wasn't done yet, though; he righted himself in midair and grabbed Samus with one of his talons. He spun around and launched her at the wall.

Samus returned to her normal form as she flew through the air, and righted herself to leap directly off the wall. She checked her missile reserves and swore inwardly. Only 1 Super Missile and 24 normal missiles left…

She fired off her last Super Missile, catching Ridley off-guard and sending him spiraling to the ground. Just before he collided with it, though, he spread his wings and glided for a short time before swooping upward again.

Ridley now flew up above the broken ceiling, raining down fireballs from above. Samus tapped into her Metroid DNA and followed him, levitating to his height. The two circled each other, firing off missiles and fireballs in succession. The bounty huntress kept a close eye on her missile reserves, and finally, they dropped to zero. At that point, she resorted to charged shots.

Ridley, sensing that he was gaining the upper hand over Samus, made an attempt to grab at her again. She flew back, firing off another charged shot at his face.

The sun was beginning to rise, shining a brilliant gold over the landscape, and somehow, Samus felt that this was a sign that the battle was over.

She flew above him and changed to morph ball form. There, she left behind a Power Bomb. She flew out of the way, and it exploded, sending Ridley spiraling down to the ground.

With a large crash, he hit the floor and was still. Samus knew that he would never get up again.

-=-=-

Ashen Feather and Odius reentered the lobby just in time to see Samus disappearing through a door. Odius glanced down at the body of Ridley, laying face-up on the floor. "You follow her," he told the Chozo, who nodded.

Odius walked down to the space dragon's body and knelt down beside it. Just then, he noticed the wing twitching.

"Still alive, aren't you?" Odius chuckled. The space dragon opened one eye.

"Please," he croaked, staring at Odius. "Kill her. Kill Aran…"

Odius shook his head sadly. "I'm not going to do that for you, Ridley. I don't answer to anyone. High Command is no more, and your time is almost up."

"This isn't fair…" Ridley choked out.

Odius laughed at that. "You brought this on yourself, you know. Arvo warned you not to attack K-2L. You refused to listen and had him almost killed. Then you went and attacked it…and made your own worst enemy."

"Please," Ridley whimpered. "Won't you help? The backup of my mind is still intact…my replacement body can…"

"I already killed your replacement body," Odius replied curtly before continuing. "Not only did you make your own worst enemy, but you also set the Space Pirate rebellion in action. Those of us who agreed with Arvo saw that you were wrong…but we also saw that yours was the direction that the Space Pirate Empire would be moving in. We didn't want that. Your attack on Arvo gave birth to our cause."

"I can't die," Ridley whispered. "I can't. This isn't right. This isn't fair. You have to help me. You have to."

Odius gave the space dragon one last, sad glance before following after Ashen Feather and leaving Ridley to die.

-=-=-

"These stairs are rigged with explosives," Adam warned Samus before she set foot on them. Silently, she levitated into the air and descended them without touching the steps.

"There must be something important down here, then," she replied finally. She had locked the door behind her, not wanting anybody to follow her. Before that, though, she had retaken the Protector's Suit. Out of respect for Wesley, she had put her old Power Suit on him.

At last, after five minutes of descent, they reached the bottom. Five large computer consoles stood stationed around the room, and Samus realized what they were. "These contain the minds of the High Command members," she muttered.

She punched her arm cannon through each of them, destroying them once and for all.

"There," she said, satisfied. "Let's see them come back now."

She turned to leave when she heard a strange noise.

Turning around, she saw none other than White Voice.

"What are you doing here?" she asked.

"Kill it," he whispered, somehow speaking. "I can't control it for long…I'm using it to stay alive, but soon…"

"What?" asked Samus.

"The X!" he hissed. "It has me!"

Samus nodded in understanding and fired a beam shot at him. He sighed contentedly and fell to the ground, and the X floated out of him. Samus tried to escape, but the Metroid-resistant parasite flew into her.

Gasping, she fell to her knees, believing this to be the end.

But then…

The strange script filled her visor again, and the influence of the X seemed to just disappear.

"What the…what just happened?" wondered Samus aloud.

"It's the last resort," murmured White Voice. His life force was beginning to wane, but he was still alive for now. "When all other methods fail…Zebes is no mere planet. It is the method by which we intended to destroy all the X Parasites once and for all. The program within your suit…when it, the Protector's Suit, and the Protector of the Galaxy herself return to the core of Zebes, all the X Parasites in the universe will be drawn to that location…and be destroyed. As soon as the Chozo discovered that the X Parasites had made a recovery, they returned Zebes to the realm of the living."

"Why did the X-Brain have it, though?" Samus asked.

"The X Parasites must have discovered it and realized its purpose. Intending to prevent you from obtaining it, they entrusted it to the most powerful of them all."

Samus nodded her understanding.

"There is one more thing, though…" White Voice continued, his voice beginning to fade. "When the program is activated and the X Parasites destroyed…Zebes will disappear, along with the Protector of the Galaxy. You will cease to exist in this realm."

With those final words, White Voice died.

Samus stood there silently, absorbing all the information that the Chozo had told her. She then went back up to the lobby.

-=-=-

Odius and Ashen Feather were there to greet her.

"Samus!" Ashen Feather cried, hugging her. "You did it!"

Samus hugged her friend back, the words of White Voice still weighing heavily on her conscience. She resolved not to tell them about it.

"I destroyed the minds of all the High Command members, too," she said.

"That's good," Odius replied, nodding. "We killed the three senior members, along with Ridley's replacement body. High Command is no more."

Samus nodded her satisfaction.

"What happened to Wesley, though?" asked Ashen Feather, frowning. Samus sighed. "…He's dead," she said grimly. "He…sacrificed himself so that I could defeat Ridley."

Silence.

"He was a good man," Odius said finally. "He'll rest peacefully knowing that he helped you succeed."

Samus nodded. "Yes. I suppose so."

They sat down and told each other what they had gone through. Samus, of course, neglected to mention her conversation with White Voice. When Odius and Ashen Feather mentioned the cloning vats, Samus' brow furrowed in thought.

"Adam," she said later.

"What is it, lady?"

"The Galactic Federation…it'll need a new leader, won't it?"

"I suppose so."

"…And they don't know that Rodriguez is dead yet…and we have his body…"

"Stop it," commanded Adam. "I can see where you're going with this, and I don't want any part in it."

"If someone competent doesn't take charge, the Federation could remain just as corrupt as it is now," Samus countered.

"I died, lady. I died an honorable death. I'm satisfied with it. Don't force me back into life like this. It's just not right."

"Sometimes, Adam," Samus said, "we have to sacrifice our peace of mind for the greater good. I'm certainly not pleased with having to lead a life of killing…but I did it because it was the right thing to do."

Adam finally relented. "Fine. But it's only because I must. Once the Federation is on the right track, though, I intend to step down immediately."

Samus nodded her satisfaction. "I'm not asking you to do anything else."

They took a sample of Rodriguez's uncorrupted DNA from the ship, and put it into the central pod. They disconnected all the other pods from it except one, and entered Adam's mind into it.

Before long, they had a perfect copy of Rodriguez as he had been before being infected with the Metroid DNA, with Adam's mind.

"It's going to take some time getting used to this again…" Adam commented, moving unsteadily with Rodriguez's body. "I forgot that it was so cumbersome having to breathe…"

"What will you do, Odius?" Samus asked, turning to the Space Pirate. He shrugged. "Same thing as Adam, I suppose. I'll put the Space Pirates on the right track, then step down…it'll be difficult, more difficult than Adam's duty, but I'm confident I can win over the main population."

Samus turned to Ashen Feather. "And you?"

"I've done my duty already," the Chozo said simply. "My job was to guide the Hatchling, to assist her in saving the universe. And, not to sound arrogant here, but I think I've done a pretty good job of it." He frowned. "But…we still haven't gotten rid of the X yet…"

"Don't worry about that," Samus said. "I have a feeling that the X won't stay a problem for long."

-=-=-

"We're here live at the Federation capital, where President Martin Rodriguez has an announcement to make. Ex-convict Samus Aran is at his side, after having been pardoned as soon as the president returned."

The clamor in the crowd died down at the president took the stand.

"Ladies and gentlemen," he declared. "Over the past three and a half decades, the Galactic Federation and the Space Pirate Empire have been perpetually at war. I am pleased to announce that this war is over."

There was much shouting for clarification and explanation until the president signaled for the audience to be silent.

"Just a few weeks ago, a treaty was signed, calling for cooperation between the pirates and the Federation. We waited to see how this treaty would turn out before announcing it to the general public, and it is clear now that we have established a lasting peace. Ladies and gentlemen, please welcome Space Pirate High Commander Odius."

There was some hesitant clapping among the audience as the pirate took the stand.

"Over the past thirty-five years, the Space Pirates have come to stand for murder, destruction, and evil," Odius began. "It is my intention to make that perception nothing but a faded memory…"

-=-=-

Two weeks had passed since the truce had been announced. Samus had become a familiar face at the Federation capital, always at the president's side, yet never speaking. Rumors flared that she was in an affair with the president, but she didn't let it bother her.

Odius, too, made periodic visits to the capital, bringing news on the state of the Space Pirate reconstruction. There had been some rebellion, particularly among Ridley's former troops, but most of the population seemed pleased with the changes he was instigating. They had considered changing their name to rid themselves of the image people had of them, but decided against it; that would be too pretentious.

Several days earlier, an unfamiliar vessel arrived at the Federation capital. Samus was surprised – and relieved – to learn that it contained the Etecoons and Dachoras. How they had obtained that vessel, she was unsure of…they were creatures of mystery, that was certain.

Adam had shut down all of Rodriguez's former experiments. After the Valhalla had been evacuated, it was rigged with explosives and detonated. The facility on Lycas shared a similar fate. Much of Rodriguez's staff was fired, as well, especially after Adam looked into their backgrounds.

Ashen Feather had not been seen since they had left Earth. They assumed that he had joined the rest of the Chozo in the next realm.

At last, Samus decided that she had waited long enough. She found her old ship within one of the Federation's hangars, and, without saying good-bye to anybody, departed for Zebes.

-=-=-

The rain trickled down her visor as she stepped out onto Crateria. She glanced up at the sky. The stars were bright tonight, despite the heavy downpour.

She walked into the caves, prepared for X Parasite attacks. They didn't come…perhaps they were resting. Perhaps they sensed that their time had come. She toyed with this idea before discarding it.

Before long, she came across the mangled bodies of ten Metroids. She felt a pang of regret…but also a feeling of pride as she saw the dried out husks of each SA-X.

Tourian…that was her destination. The elevator was still broken; she hopped down the shaft, not caring. She wouldn't be hurt now, anyway.

She landed gracefully on her feet, and continued walking. Soon, she reached Mother Brain's chamber. It was strange…when she had revisited it after destroying Mother Brain in the past, it was always in poor condition. This time, it was as if nobody had ever set foot in there.

There was a large, gaping hole where Mother Brain used to be, and Samus knew that she had to go down it.

As she fell, she began to feel cold. Not unpleasantly cold, though…this felt nice. Like a spring breeze…

The familiar script ran across her visor once again, and she was surprised to find that this time she could read it.

She read the script over several times, and understood what she had to do.

She called to mind all the people who had been lost to her: her parents…Tarus Wesley…White Voice…even Adam's original body. As she did so, the cold turned to warmth.

The script began to glow blue.

And, one by one, Samus let each of them go, her sorrow departing like the wind. She didn't forget them; she merely let their memory rest.

Her sorrow scoured the four corners of the universe, gathering up all the X Parasites in existence and bringing them back to the place where Samus waited, her eyes closed, her limbs spread serenely. And then, without reentering Samus, her sorrow disappeared. The blue glow of the script became stronger.

And then, Samus remembered her anger; anger at Ridley, anger at the Space Pirates, anger at Rodriguez and the Federation. She let that go as well, and it bound the X Parasites to her before it disappeared.

Finally, she remembered her joy; joy at having found a family with the Chozo, joy at having reunited with Adam, joy at meeting Ashen Feather and White Voice. These memories, she kept, and their influence radiated outwards.

The script turned a bright white, and one by one, the X Parasites turned this bright white as well and disappeared.

_"The end of the X will be by emotion rather than violence."_

And as the final X disappeared, the warmth within Samus spread through her whole body.

And then, she found herself in the next realm, where Old Bird, Ashen Feather, White Voice, and even Tarus Wesley awaited.

**//////\THE END/\\\\\\**


	13. Epilogue

**EPILOGUE**

An aged, tired-looking old man stared down at the abandoned settlement. Vegetation was beginning to reclaim its lost territory; the old homes now harbored only leaves and vines. But, as if repulsed by it, no plants grew in one specific area, marked by irremovable burn marks.

"I thought I'd find you here."

Adam glanced down from his vantage point on a tree branch. The familiar face of a Space Pirate, almost as wrinkled as his own, greeted him. He raised his hand half-heartedly in greeting.

"Mind if I come up?" Odius asked. Without waiting for a response, the former High Commander hauled himself up next to Adam.

In silence, they stared across the landscape for several minutes before Odius finally said something else.

"You were probably the closest thing she ever came to loving someone, you know."

Adam took a sidelong glance at the pirate. "Don't be crazy," he replied.

Odius shook his head. "I mean it. I may not have known her for as long as you did…but I could tell. If there was one person in the universe that she would love…it would be you."

Adam sat there quietly, an unreadable expression on his face.

Odius sighed and turned back to the view below them. "It's beautiful, in its own way," he murmured. "All these plants thriving here…you'd never think that it was once a battleground…except for…well, that…" He directed his gaze away from the scorch marks.

"…Were you there?" Adam asked quietly.

Odius refrained from looking at the former Federation President. "Yes. I was there."

"Did you…?"

Odius shook his head. "Of course not. I didn't fire one shot during the attack. Lucky I didn't get caught not killing and plundering," he added, laughing uncertainly. At Adam's disapproving look, he immediately stopped.

"What if…" Adam began hesitantly. He glanced at Odius before continuing. "What if things had been different?" He gestured to the burn mark on the ground below.

Odius sighed. "If things had been different, then we'd probably be trying to kill each other right now. If things had been different, we'd probably never have known her."

"Do you really think that?" Adam asked. Odius nodded.

"I don't," Adam replied. He lifted his gaze to the skies. "I think…I think she could have done it anyway. She was special…she didn't need enhancements or technology. She could have done it on her own…"

"You promised you'd never get sentimental," Odius pointed out dryly.

"Sorry," Adam said, grinning and wiping tears from his eyes.

"But it's hard to believe, isn't it? It's been seventy years since it all began…seventy years since the first pirate attack…" Adam commented.

"And how old would she be now?" asked Odius.

"Sixty-two…she was born eight years after the raids began…a pity that so many innocent young lives are born into times of war…"

Adam sighed.

"She told me once that she wanted to return to this place at some point…I don't know if she ever did."

"Maybe it's better that she didn't," Odius mused. "She wasn't one to focus on the past. She always looked to the future."

Adam nodded. "That's true. That's true."

"Do you think anyone will ever live here again?" asked Odius.

Adam shook his head. "No…I made sure of that during my term as president. This is where the protector of the galaxy was forged in fire. It should not be desecrated."

"I spoke to Ridley before he died," Odius said suddenly. Adam glanced at him again.

"I made sure that he knew that he brought about his own downfall. This is where it happened…I just thought it would be fitting for me to mention that."

Adam continued to stare. "Ridley was a monster," he said. "I don't think he was capable of feeling sorry for anyone…even for himself."

"I don't know…" Odius said. "I was there when it all happened, and, before he attacked…it almost seemed as if he felt sympathy for her…even if it was only for an instant…"

Adam shrugged. "Sometimes we see things that aren't really there."

Odius sighed. "I suppose you have a point…but I know what I saw."

Changing the subject, he gestured to the plants. "It's strange, isn't it? It's like they know that the burn mark is a sacred spot."

"Maybe they do know," Adam contemplated.

"Her parents would be proud," Odius murmured softly.

"I'm sure they are," Adam replied. "Prouder than any parents have ever been and will ever be."

"She was an extraordinary woman…"

"Beyond extraordinary."

"Beyond extraordinary," Odius agreed.

Adam took something out of his pocket. "This is the last trace of her," he said. "Once I bury this, it'll be like she never existed…"

"What is it?" asked Odius.

Adam smiled, tears coming to his eyes again. "The chip from her helmet…the one that contained my conscious."

He hopped down from the tree and began the walk to the burn mark on the ground. Once there, he buried it in the center.

"Thank you, Samus," he murmured softly. "For everything."

Hundreds of years passed. Governments toppled, wars were fought, disease raged through the galaxy, and hate ran rampant. But none of it ever reached the surface of K-2L. But the memory of Samus Aran lived on. She became a symbol of hope, and when things were at their bleakest, people would remember her, and they would realize that the darkness would pass…as it did.

One plant managed to sneak its way into the consecrated spot where Samus Aran's mother died and where the Protector of the Galaxy was born.

A lone tree towered above all the others, keeping its silent vigil over the land.


End file.
